Aiming at the problem of insufficient research on deformation characteristics of cement mixing piles composite foundation under subgrade filling at present, based on a construction case of railway subgrade filling reinforced by cement mixing piles in marine soft soil areas of China, this study monitored the deformation of composite foundation for cement mixing piles during subgrade filling. The deformation characteristics of composite foundation of cement mixing piles under subgrade filling were analyzed, and suggestions for subgrade filling rate control and cement mixing piles reinforcement scheme design were provided. The results show that the compression of the foundation reinforcement zone accounts for 56.1% of the total settlement under subgrade filling, and the maximum settlement rate is 2.4 mm/d. The lateral deformation of plain fill and silt layer is significant, and the maximum lateral deformation rate is 4.6 mm/d. The strata within 7 m from the foot of subgrade slope and above the depth of 5 m are greatly disturbed by the construction of subgrade filling. The lateral deformation rate of the slope is closer to the control index than the settlement rate of the foundation and the subgrade filling rate should be controlled mainly by controlling the lateral deformation rate of the slope. In this construction case, the cement mixing piles reinforcement scheme can meet the control requirements for post-construction settlement of subgrade of all railway types, the design of cement mixing piles in similar projects mainly controls the influence of subgrade filling construction on adjacent structures.