The aesthetic appearance of the microscopic instruments can reflect the advanced qualities, while improving the pleasure of the operation experience. The establishment of aesthetics indexes and evaluation method of microscopic instruments can quantify the beauty degree of instruments’ appearance, and make the objective formal beauty correspond with the subjective feeling beauty, so as to effectively guide the aesthetic design of microscopic instruments. First, based on the features of microscopic instruments, the rules of beautiful form, and the beauty calculation model of Ngo and Birkhoff, seven quantitative indicators for the beauty evaluation of microscopic instruments were constructed such as Balance, Symmetry, Proportion, Rhythm, Unity, Order and Color. Then, the correlation among 7 beauty indexes was analyzed, and the fuzzy evaluation matrix R for calculating products’ beauty was established. Finally, taking four types of laser scanning confocal biological microscopes as samples, the subjective and objective comprehensive evaluation was made by applying aesthetics indexes and the fuzzy comprehensive evaluation method. The results show that the fuzzy comprehensive evaluation vector of the sample 4 designed by Harbin Institute of Technology is B4 = [0,0. 353 4, 1. 042 5, 0. 888 3, 1. 256 2], which indicates that its beauty grade is higher than others, and it has a better performance of unity and order.