In this work, we perform a systematic lattice QCD study of the intrinsic, rapidity-independent soft function within the framework of large momentum effective theory. The computation is carried out using a gauge ensemble of $N_f=2+1+1$ clover-improved twisted mass fermions. After applying an appropriate renormalization procedure and the removal of significant higher-twist contamination, we obtain the intrinsic soft function that is comparable to the one-loop perturbative result at large external momentum. The determination of the non-pertrubative soft function from first principles is crucial to sharpen our understanding of the processes with small transverse momentum such as the Drell-Yan production and the semi-inclusive deep inelastic scattering. Additionally, we calculate the Collins-Soper evolution kernel using the quasi-transverse-momentum-dependent wave function as input.