Focusing on the huge consumption of time and space and the absolute comparison result of Basic Block (BB) resulted from one-to-one mapping of basic block in traditional file structural similarity detection technique, a method based on dividing thought was proposed to accomplish structural comparison of binary file. Firstly, the small primes algorithm which is used to compare the basic block was improved to classify the basic blocks in a function, then the similar rates of basic blocks were obtained by combining with the weights of basic block signature and attribute, so as to get the final function similar rate and final file similar rate. In the comparison with the absolute comparison method which does not consider the partition at the similar rates of function, this proposed method has certain advantages in efficiency and accuracy. The experimental show that the proposed method improves the accuracy of comparison, and reduces the comparison time, it is more feasible in similarity comparison of binary files.