To accurately evaluate the safety of foundation pit construction in soft soil area and its impact on the surroundings, the time and space influencing factors during excavation cannot be ignored. In this paper, based on the excavation of a deep foundation pit in the soft soil area of the Yangtze River floodplain, a 3D finite element model was established considering the combination of bottom-up and top-down constructions, and the calculated values of horizontal displacement of the diaphragm wall were compared with the measured values to verify the reliability of the finite element calculation. Based on theoretical analysis, numerical calculation and measured data, the influence coefficient of corner effect and equivalent horizontal resistance coefficient were used to measure the influence of spatio-temporal effect on the deformation of supporting wall, and the calculation method of the diaphragm wall deformation considering spatio-temporal effect was proposed. The necessity of the spatio-temporal effect and the rationality of the proposed method in the design of foundation pit in soft soil area were verified by engineering examples. The results can provide beneficial reference for the calculation of deep foundation pit deformation in soft soil area.