In this paper, a design method of the simulation program for HILS(Hardware-In-the-Loop Simulation) system is proposed. The present method consists of definition of requirements for HILS, development of specifications, and implementation of the program to satisfy the specifications. In the implementation of the program, the application of hardware interface and the concept of structural modularization are proposed to satisfy the specifications. The concepts of CSCI(Computer Software Configuration Item) and encapsulation are used for structural modularization. The proposed method was practically applied to the development of the simulation program for the efficient operation in HILS of an anti-ship missile system.