The invention provides an ecological risk assessment method for a nature reserve. The ecological risk assessment method comprises the steps of S1, identifying ecological risk types of the natural reserve and constructing evaluation indexes of different types of ecological risks; S2, respectively calculating the weight of each evaluation index corresponding to different ecological risks of the natural reserve by adopting a mean square error weighting method, and metering the weight of the natural reserve harmed by different ecological risks; S3, visually evaluating the ecological risk indexes of different types of ecological risks of the natural reserve by adopting a GIS software platform to obtain an ecological risk index spatial distribution pattern diagram of different types of ecological risks; and S4, multiplying different types of ecological risk indexes of the natural reserve by the hazard weight of the ecological risk indexes on the GIS platform to obtain a comprehensive ecological risk index of the natural reserve, and grading the risk indexes to obtain a comprehensive ecological risk grading graph of the natural reserve. The method has the advantages of being accurate, scientific, comprehensive, systematic, wide in application range and the like for the ecological risk of the natural reserve.