As a new type of agricultural production and management organization, scientific and objective evaluation of the performance level of agricultural machinery cooperatives is of great significance to the healthy development of agricultural machinery cooperatives and the promotion of rural revitalization. Combined with the development status, characteristics and evaluation needs of agricultural machinery cooperatives in the new stage, a new method for designing the performance evaluation index system based on the six-dimensional balanced scorecard (6D-BSC) was created, covering business scale, learning and growth technical effects, economic effects, beneficiary groups and green development. A weight calculation method was created based on the method of principal component analysis (PCA) and the weight value of each index was determined according to it, and the performance evaluation criterion based on fuzzy multi-criteria (VIKOR) method was improved. The evaluation index system will be more reasonable and the evaluation results become more accurate based on the new evaluating method combined with the abovementioned three improved methods. Total agricultural cooperatives in each of 14 cities in Heilongjiang Province were taken as research objects, and evaluation results show that the overall performance level of agricultural machinery cooperatives of each city can be divided into six layers. Among them, the overall performance level of agricultural machinery cooperatives in Qiqihar is the highest in the first level, the operation effect of agricultural machinery cooperatives in Suihua is prominent in the second level, and the overall performance level of agricultural machinery cooperatives in Harbin and Heihe is relatively high in the third level.