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Forest biological disaster control (FBDC) is appealing the attention in China and even across the world, while the control system plays a pivotal role in the entire control work. The survey-based comprehensive indicators system was developed to evaluate the perceived effectiveness of the entropy weight model and the perceived responsibilities of the FBDC system of China from the perspective of government administrators at the province-, prefecture-, and county- levels. Ordinary Least Square (OLS) and Simultaneous Equations Models (SEM) were further developed to quantitatively analyze the affecting factors of the perceived effectiveness. The results indicated that the perceived effectiveness of the FBDC system in China was relatively low, with a value of 47.18 (the range is 0–100). In specific, the county level has the highest value of 48.85, while the province level has the lowest value of 42.99. The major limiting factors perceived are the insufficiency of the funds and employees. In addition, the intelligentization level, the implementation of the quarantine enforcement, the infrastructure construction, and the involvement of the local communities also need to be further improved. The salary does not positively affect the perceived effectiveness, while administrators with higher education levels and ages usually have higher salaries. Furthermore, compared with the province- and prefecture-level agencies, the county-level agencies have higher perceived effectiveness and more perceived responsibilities with higher workloads. Thus, future policies are suggested to focus on diversifying the investment sources, refining the employee recruitment and promotion system, and paying more attention to the county-level agencies. The results of this study could help to enhance the understanding of the FBDC system of China, hence improving the control efficiency and reducing the economic loss caused by forest biological disasters in China.