The space-time effect on the excavation of coastal soft soil foundation pit has an important impact on the stability of the foundation pit. In order to control the deformation of foundation pit in soft soil area, the ultra-long deep foundation pit project of Qianhai Station of Guangzhou-Shenzhen Intercity Railway is taken as an example, and the space-time effect of the ultra-long foundation pit in the excavation process is researched by analyzing the horizontal displacement of the enclosure structure, the surrounding surface settlement, and the supporting internal force during the excavation process. The results show that: (1) the spatial effect is obvious in the excavation of the foundation pit, and the horizontal displacement of the enclosure structure in the middle of the foundation pit is 18.3% larger than that at the end; (2) the difference in displacement of the enclosure structure will lead to the differential settlement of the soil at the edge of the pit, and the maximum longitudinal settlement difference of the foundation pit reaches 17.5% when it is at the same distance from the edge of the pit; (3) during the construction interval, the displacement and stress of the supporting structure under the same working condition will increase with the growth of time; (4) during the curing period of the first four concrete internal supports in the soft soil layer, the maximum horizontal displacement of the enclosure structure increases by 31.2%, 30.9%, 23.2% and 14.4%, respectively; (5) the space-time effect of foundation pit excavation should be reasonably considered in the project.