To verify whether the parameters of the domestic proton injector meet the requirements, a beam diagnostic system was designed to measure the current, emittance, energy and energy spread of the domestic proton linear injector beam. This beam diagnostic system has the main functions of measuring the emittance by variable focus method and measuring beam energy and energy spread by analyzing magnet. The beam transport line design software Tracewin (version 2.11.4.1) was used to design the physical system beam line, and the accuracy of the beam diagnostic system to measure the emittance and energy of the proton beam was simulated and calculated. Since the beam accelerated by RFQ-(APF)DTL is a “trailing” non-ideal bunch , it is necessary to analyze the influence of the non-ideal bunch on the emittance and energy measurement of the beam diagnostic system. The analysis of the simulation calculation results shows that compared with the ideal bunch, the non-ideal bunch has greater impact on emittance measurement accuracy and smaller impact on energy measurement accuracy of the beam diagnostic system.