In the petrochemical production system, the high-risk items malfunction may lead to major accidents so that the risk level of the items has become the highest focus of attention for the enterprises in petrochemical industry. Based on structural composition and risk relationship, a risk evaluation framework of the petrochemical production system can generally be divided into subsystems (SS), components and parts (CP), failure modes (FM), risk types, and risk factors. So it is a characteristic of multilevel, complex structure, and lack of evaluation criteria that the evaluated object has in the process of risk evaluation. However, there are few targeted modeling and calculation methods to carry out quantitative risk evaluation in the face of the evaluated object. In order to achieve risk quantitative evaluation of the complex structure hierarchical system, a multilevel Borda model (MLBM) is presented innovatively by us based on the traditional Borda method in this study. Moreover, the MLBM are applied to realize quantitative risk evaluation of the main structure system of truss type crane on the offshore platform. In this case study, the equivalent risk value (ERV) and risk priority number (RPN) of the evaluated object with multilevel, complex structure, and inadequate evaluation criteria are calculated and the risk ties in the RPN are effectively reduced. Then, the quantitative risk results can clarify the risk level and distribution of the high-risk items throughout the production system and provide data support for the development of risk control measures to better protect the production safety. Hence, the feasibility and practicability of the method are verified with the case study. The MLBM can be used to solve other comprehensive evaluation problems with a complex hierarchical structure as well.