In this paper, Petri net theory is taken into analyzing the Virtual Experiment (VE) in the Virtual Experiment Environment (V.E.E.). After applied the Petri net to V.E.E., the V.E.E. then can monitor the experiment progress and measure the learning effects of students when the students are doing experiment. Petri net is an approach that can be used as a visual-communication aid similar to flow charts, block diagrams, and networks. Therefore, the experiment steps are easily modeled by Petri net. According to the data which is collected by the V.E.E., there are two major error types that a student might make during an experiment. The first error type is the procedural error and the other one is measuring error. In the end of this paper, an experiment system is implemented. There were 72 3rd year students in junior high school involved in the experiment. In this experiment, we did both of pre-test and post-test in order to make sure the Petri net-enhanced V.E.E. is useful.