Based on the conventional analytical method on wiretap channel model, the physical-layer security of intensity shift keying (ISK) quantum-noise randomized cipher (QNRC) systems is analyzed quantitatively. The wiretap channel models for the key and the data in ISK-QNRC systems are established respectively. The secrecy rates are employed to evaluate the physical-layer security level of both the key and data. Further, the maximal achievable secrecy rate of ISK-QNRC system is proposed, which guarantees the secrecy of the key and data. In order to further optimize the security of ISK-QNRC systems, the impacts of various system parameters and cases on secrecy rates are assessed and compared in detail. The simulation results indicate ISK-QNRC system combined with proper channel codes can realized high-speed and long-haul anti-interception communications. The maximal achievable secrecy rate of ISK-QNRC system is constrained mainly by the security of the running key in general cases. It is helpful to choose the proper power of mesoscopic quantum state, gain of optical amplifier at the transmitter and number of bases for improving the security performance of ISK-QNRC system.