The invention discloses a code homology analysis method based on a function call relation graph, which comprises the following steps: generating a parent graph by a function call relation graph basedon the code; calculating a relative editing distance between the function call graph and the parent graph, the semi-variance of the matrix corresponding to the function call graph and the degree distribution order value of the function call graph; using at least one of a relative edit distance, a semivariance value, and a degree distribution ordered value to analyze code homology. Relative editingdistance determines the overall program orderliness and disorderliness from the perspective of program organization code homology analysis; Semi-variance value determines the depth-first or breadth-first programming habits of program writers from the perspective of code logic code homology analysis to; The degree distribution order value carries on the code homology analysis from the statisticalangle, judges the program call frequency distribution. By synthesizing the three indexes and distinguishing the design and invocation characteristics of the function, it has a better performance in the field of code traceability.