The smoothness of the track structure has always been an important issue affecting the safe and smooth operation of trains, especially for high-speed railways which have more stringent requirements. To ensure that the track structure has a durable and stable high level of smoothness, the subgrade supporting the track structure must possess characteristics such as minimal post-construction settlement, small uneven settlements, and good stability under dynamic loads. To meet these requirements, high-speed railways built in soft soil areas often adopt ballastless track pile-net or pile-raft composite foundation types to satisfy the needs for smooth, safe, and comfortable high-speed travel. Although the aforementioned measures are very effective in controlling the settlement deformation of the high-speed railway subgrade, due to the characteristics of soft soil such as high water content, large porosity ratio, high compressibility, low shear strength, poor permeability, significant rheological properties, and low bearing capacity, it often results in continued development of subsidence in the ground for quite a long time after the completion of the project. This has led to a series of environmental disease problems. With the large-scale construction and commissioning of high-speed railways in China with speeds exceeding 300 kilometers per hour, some sections of soft soil subgrade have successively experienced localized subsidence, uneven settlement, rail surface inclination, and displacement. This not only seriously threatens the operational safety of high-speed trains but also requires a significant amount of manpower, physical resources, and financial investment for the treatment of these diseases. Therefore, exploring the occurrence mechanism, development law of soft soil subgrade settlement diseases in high-speed railways, as well as how to quickly reinforce and control deformation of the diseased subgrade while ensuring the operational safety of high-speed trains, has become one of the most concerned issues for engineering construction management, design, and on-site construction units. This achievement mainly relies on the Shanghai-Hangzhou Passenger Dedicated Line subgrade settlement disease treatment project. A thorough study has been conducted on the settlement and deformation characteristics of high-speed railway pile-raft composite subgrade in deltaic soft soil areas, as well as rapid reinforcement and control deformation techniques. Starting from the dynamic characteristics principle of soft soil, the mechanical mechanism of settlement and deformation under the action of moving load from a 350 km/h high-speed train for ballastless track pile-raft composite subgrade was analyzed and studied; combined with numerical simulation, the long-term operational stability of the pile-raft subgrade at the K1 worksite project was analyzed, and an appropriate foundation reinforcement scheme was selected; through the analysis of the disturbance dynamics effect of static pressure grouting in soft soil, a reinforced grouting method and process suitable for operating high-speed railways were studied; combined with indoor mechanical properties tests, parameters such as suitable grouting percentage, slurry water-cement ratio, and reasonable setting time were provided; through field grouting tests, the intrinsic relationship between grouting parameters and stratum disturbance deformation was obtained. Based on this, the control technology for grouting subsidence reduction of ballastless track pile-raft composite subgrade under uninterrupted traffic conditions was studied, and ultimately a set of design theories and rapid construction optimization technologies for grouting subsidence diseases of passenger dedicated line ballastless track pile-raft subgrade were formed. The achievements of this topic have been fully applied and verified in the treatment project of soft soil subgrade settlement diseases of Shanghai-Hangzhou High-speed Railway. While ensuring the effectiveness of soft foundation treatment, a significant amount of investment has been saved, creating direct and indirect economic benefits of 3 million yuan. During the implementation process of this topic, 12 academic papers have been published in important domestic and international journals. The results of this topic are the first systematic research on the treatment of high-speed railway subgrade settlement diseases in operation in China. The research results further improved the existing theoretical structure design and reinforcement technology of subgrades, which has important academic value. Moreover, it also provides a reference and reference for the construction and operation management of high-speed railway subgrades in other soft soil areas in the future.