The invention discloses an intelligent debugging method and system based on a handshake protocol, and the method is used for carrying out the intelligent debugging of at least one numerical control machine, and comprises the following steps: S1, obtaining the measurement model parameters of the numerical control machine, and receiving the actual measurement data of a machining part collected by the numerical control machine, wherein a handshake protocol based on a system macro variable is established with a numerical control machine table to receive actual measurement data, collected by the numerical control machine table, of a machined part; S2, according to the measurement model parameters, converting actual measurement data, collected by the numerical control machine, of the machined part into measurement data in a standard format; S3, solving an optimized compensation value of the numerical control machine according to the measurement data in the standard format and the measurement model parameters; and S4, transmitting the optimized compensation value back to the numerical control machine, so that the numerical control machine is adjusted according to the optimized compensation value. According to the invention, the problem of machine adjustment in the prior art is solved.