Modern manufacturing systems consist of highly automated manufacturing devices, and they are controlled by complicated PLC programs. To make sure the achievement of the control objectives of a manufacturing system, it is very important to monitor the dynamic system behaviors of the manufacturing system. In this paper, we propose a monitoring methodology of a PLC program based on the Software In the Loop Simulation(SILS), which makes use of the time gap information between PLC signals. The errors relevant with PLC signals can be found using the proposed methodology, comparing a normal PLC signal trajectory with a target PLC signal trajectory. The proposed methodology has been implemented and tested with simple examples.