Due to the limitations of detailed experimental data for large scale metabolic networks, structural analysis of these networks is a growing research topic in bioinformatics field. Among several available structure-oriented approaches, Petri nets has proved to be particular efficient tool, and thus is employed for studying P. Pastoris metabolic network in this study. After a brief introduction about the conceptual framework of Petri nets analysis, we give the first in silico Petri nets model of P. Pastoris metabolic network, we also calculate, analyze and classify the p, t invariants in the model based on their structural capability and biological significance.