Utilizing the complex network theory to mitigate vulnerabilities mitigation in integrated energy systems is significant for enhancing the resilience of sustained energy supply, especially against deliberate physical attacks and natural disasters. To implement more precise preventive measures for vulnerable components in integrated energy systems, this paper proposes a weighted betweenness-based protection optimization model for safeguarding vulnerable segments. The model aims to minimize the weighted betweenness loss incurred post attacks and damages, while simultaneously considering strategies such as establishing backup nodes and backup lines, enhancing physical protection of nodes and lines, and adding new lines. These strategies are subject to constraints such as protection requirements, budget limitations, and constraints on the types and quantities of new lines. The model optimization provides the optimal protection strategies within the allocated budget. To address the complex betweenness computations and non-linear objective functions, the model is formulated as a bilevel structure based on the nature of protection measures first. Then, the lower-level model is solved using a local linearization technique, and a “genetic-mixed integer linear programming” algorithm is proposed for solving the model with high precision and efficiency. The simulation results demonstrate that under conditions of equivalent attack and damage, the system with the optimal protection strategy achieves reduction of 45.37% in weighted betweenness loss compared with that without protection. The optimal strategy outperforms the other five protection strategies considered within the allocated protection budget.