Smart contract is a computerized protocol for informationally disseminating, validating, or enforcing a contract when specific conditions are met. The similarity calculation of the graph is used to compare the similarity between different smart contracts to detect potential malicious contracts or plagiarism. At present, most of the secure multi-party calculations of graph structure similarity are designed under the semi-honest model, which cannot resist malicious enemies. In this paper, a new coding method based on prime number is proposed and a semi-honest computing graph similarity protocol is designed by using ElGamal Threshold encryption algorithm. Then we analyze the possible malicious attack behavior in the semi-honest model protocol and design the secret computational graph similarity protocol with the help of zero-knowledge proof cryptography tool. Finally, the real/ideal model paradigm is used to prove that the protocol is secure under the malicious model, and the efficiency of the protocol is proved by comparing with the existing schemes.