This paper is about performance measurement of supply chain in agile virtual enterprise environment with an approach that uses a new high level Petri net. Measurement of the performance of supply chain is a good indicator of the efficiency of collaboration of the enterprises involved; thus the main assembler can determine whether making changes among the collaborating partners may improve the overall performance. The approach discussed in this paper uses cost, quantity, and delivery as the key performance indicators. Due to the large number of participating enterprises and due to the dynamic nature of collaboration, classical approaches that use Petri nets are not suitable modeling supply chain in agile virtual enterprise. The new approach discussed in this paper models supply chain in an agile virtual enterprise by taking the topology of connection between the enterprises as the starting point, forming a connected system to represent the virtual enterprise. The tool AgileSIM used in this approach then generates an interim Petri net model from the connected system, replacing each enterprise by a transition-place pair, where the transition represents the production at the enterprise and the place represents the output buffer for products. The interim Petri net model is then converted into C++ code for compilation into an executable program. Thus this approach is very suitable for automating performance measurement, for example as an on-line monitor for agile virtual enterprise activities.