This paper presents a new technique of designing a control system for PWM converter based on the LabVIEW and an advanced FPGA reconfigurable embedded control and acquisition equipment, Compact RIO (cRIO). Assuming that a PWM controller is composed in the double loop structure and that the inner loop controller is given, a constructive design system that is able to make data acquisition, modeling, controller design, simulation with PC, and hardware in the loop simulation (HILS) is represented. In this approach, a key point is to obtain an equivalent linear model of the inner loop system including nonlinear components by using the closed loop identification and to use it when the outer loop controller is designed. Experimental results applied to a real PWM converter will be given as a demonstration.