Automated Rail Mounted Gantry（ARMG）is adopted in the Guangzhou Port Nansha phase IV，and ARMG has higher requirements for foundation. Due to the large thickness of undisturbed soft soil，the foundation treated with large-area vacuum preloading cannot meet the requirements for use，and secondary treatment of the rail foundation is required. Combined with the geological condition and the use requirements of ARMG，through the comparison of selection of plans，the composite foundation of cement mixing piles is used for the secondary foundation treatment of the rail. The reinforced concrete foundation beam structure + the composite foundation of cement mixing piles is adopted in the yard area rail foundation. The reinforced concrete rail slab structure + cement mixing pile composite foundation is adopted in the rail foundation in the crossing section. The reinforced concrete foundation beam + cement mixing pile composite foundation scheme can meet the use requirements of the rail with low cost and small differential settlement in the crossing section.