This paper provides the design basis and case study of soil improvement to secure the stability of jack up rig under operation and fabrication condition to effectively mitigate the risk associated with unexpected spudcan penetration. The two penetration curves of spudcan foundation are presented to confirm soil improvement influence using DMM (Deep Mixing Method) with native soil material. The results from 3D large deformation finite element (LDFE) analyses are reported on vertical penetration of skirted spudcan into multilayer clays. The LDFE analyses were carried out using the Coupled Eulerian-Lagrangian (CEL) approach and the modified simple elastic-perfectly plastic Tresca soil model. The seabed sediments were simulated as single layer soft clay with undrained shear strength increasing linearly with depth, two-layer stiff clayey sand overlying soft clay and sandy gravel. The circular block of soil improvement is partially located in the third sandy clay layer under the spudcan penetration path with specific thickness. The result with native soil condition is validated against ISO recommendation and the penetration curve for reinforced section is also overlaid concurrently. The punch-through phenomeneon predicted in the assessement by ISO method is replicated in the numerical analysis. The validation exercise of the original case shows a good agreement and the present numerical approach is capable of predicting the behavior of a spudcan penetration in multi-layered soil. The partially reinforced layer shows the load distribution during spudcan penetration. It provides the reduction of penetration depth under a given preload and seabed conditions efficiently. To ensure the structural stability of jack up rig, the uncertainties of site condition during installation should be removed such as partially trapped soft soil or soft thin layer at the footing location. The presented numerical approach can provide reasonable design basis for soil treatment to mitigate stability risk.