This study proposed a novel instructional approach, a two-stage LED simulation of Project-based learning (PBL) course with online peer assessment (OPA), and explored how to apply OPA to the different structured problems in a PBL course to enhance students' professional skills in LED design as well as meta-cognitive thinking. The participants of the study, 73 junior students were divided into two groups, OPA group (with OPA) and Traditional group (without OPA). The evaluation results were listed as follows. (1) OPA group performed better than Traditional group in concept clarification. (2) For the enhancement of LED design skills in well-structured problem solving, OPA group performed better than Traditional group. (3) For the enhancement of LED design skills in ill-structured problem solving, there was no significant difference between the performances of these two groups. (4) For students' perception about the effect of OPA applied in PBL, OPA group could benefit from inquiry learning and reflective thinking. Most students agreed that the two-stage LED simulation of PBL course was challenging and interesting and they learned useful things from the course. (Contains 6 tables and 4 figures.)