Punch-through is one of the main threats to the safe operation of jack-up units. Perforation method has been successfully implemented in engineering practice to mitigate punch-through potentials. However its research and evaluation method are still limited. With the coupled Eulerian-Lagrangian method provided by ABAQUS, finite element analysis of punch-through mitigation with perforation is carried out. The spudcan is modeled as Lagrangian domain, while the soil is modeled as Eulerian domain, among which the holes created by perforation drilling is initially modeled as void. The mechanism by which perforation mitigates punch-through potential is analyzed, which shows that the perforation drilling turns general failure mechanism into local failure mechanism in stiff-over-soft clay layers. And the effects of hole number, hole depth, hole diameter and extent are studied. It is shown that the soil plug during penetration into stiff-over-soft clay decreases with hole number, hole depth and hole diameter. Correspondingly, the efficiency of punch-through mitigation with perforation is proportional to hole number, hole depth and hole diameter. However, the effect of hole diameter on the peak resistance is relatively very small. The extent of drilling holes outside the spudcan perimeter has little effect on the peak resistance, while it has a larger effect on the post-peak resistance. An evaluation method for the efficiency of peak resistance reduction with perforation method is proposed by fitting from 75 cases of numerical simulation. It takes into account the perforation drilling area both outside and inside the spudcan perimeter; hole diameter and hole depth, which is of great significance for engineering practice.