Analyzing the vulnerability of marine fisheries under multiple disturbances from the perspective of the socio-ecological system is very helpful to solve the problem of sustainable development of marine fisheries in China. Based on the three dimensions of exposure, sensitivity, and adaptation, this paper constructed an evaluation index system and a functional model and applied an obstacle model at the same time to analyze the vulnerability and the influencing factors of the socio-ecological system of China's marine fisheries. Results show that from 2001 to 2015, the exposure index ranged from 0.3 to 0.7, showing a fluctuation trend of slow growth-declining-slow growth. Both sensitivity index and adaptability index increased from 0.1 to about 0.7, showing a constant increasing trend. The vulnerability index ranged from 0.3 to 0.8, showing a trend of horizontal fluctuation-deep declining-slow growth. The changes in the exposure were mainly affected by the climate change, land-based pollution and marine storm surge disasters. The sensitivity was mainly affected by employment dependence, fishery resource development strength and aquaculture development intensity. And the adaptability was mainly affected by the income level of fisherman families, the pressure of fisherman's life and the efficiency of the government. Based on the above analysis results, this paper provides the following suggestions: strengthening the basic research on marine climate change, controlling the development intensity of offshore fishery resources, formulating the adaptive fishery management system, and improving the social security system of fishermen.