The invention discloses a method and a system for protecting an intellectual property of software of an embedded system. According to the method, a public key is added to an embedded equipment code, an ICMP (Internet Control Message Protocol) echo request message is sent to detected embedded equipment during detection, a piece of characteristic code is encrypted by the aid of the public key in an echo message of the embedded equipment, a private key is used for decryption in detection equipment, if decryption fails, the fact indicates that embedded equipment of the opposite side at least does not copy embedded software, otherwise, the embedded equipment is our product or an infringing product, and through analysis of data in the characteristic code, if our product is not sold here, the embedded product of the opposite side is the infringing product. The system comprises an intelligent terminal, and the intelligent terminal can send the ICMP echo message, receive the echo message and perform decryption and judgment online.