The preload operation of Jack-up in complex multi-layered foundation requires an enhanced understanding of its behavior in punch-through accident and suitable safety analysis tools for the assessment of their reliability in a particular site. In order to evaluate punch-through risk, a risk-consistent method is proposed based on the model of foundation hazard and structural vulnerability. Besides, foundation bearing capacity is evaluated to quantify foundation hazard. Third, to improve the solution efficiency, higher-order moment method (HOMM)-Pushover method has been developed for assessing the structural vulnerability. In addition, case studies are presented to demonstrate the advantages of these techniques and important trends are highlighted by the results of parametric sensitivity studies. More specifically, failure probability analysis has been undertaken using improved method and the punch-through risk is evaluated quantitatively in different hazard levels. The results show that the dual uncertainty of both structure and foundation is crucial for assessment of foundation hazard and structural vulnerability. The randomness of foundation parameters is the dominant factor affecting the punch-through risk, and the risk increases with the increase of preload weight. The time-varying risk in the process of preload operation can be revealed using the risk analysis method mentioned in this paper.