The secondary consolidation of soft soil is very important for the deformation of soft soil. In the calculation of secondary consolidation of soft soil, the secondary consolidation coefficient is usually used as a calculation parameter, but this coefficient does not reflect the impact of variation for loading, and it can only apply to the normally consolidated clay. The over-consolidated clay is mostly encountered in many engineering projects. The laboratory experiments are conducted to study the secondary consolidation settlement of soft soil. The consolidation test is carried out on multiple sets of undisturbed soft clay samples. The test results show that for the calculation of secondary consolidation of soft soil, the secondary consolidation should be studied from the aspects of the strain and time; a hyperbolic form fitting is used; the strain parameters for the normally consolidated and over-consolidated soil are analyzed to establish a one-dimensional model of secondary consolidation of empirical formula. A secondary consolidation settlement calculation method is proposed considering the pressure effect on the secondary compression; the method is applied to the engineering project. It is validated that the method can be applied to the normally consolidated and over consolidated soil; it makes the consolidation of soft soil subsidence calculation more approaching the actual engineering problems.