Abstract: Both concurrence and conflict are very important conceptions in the Petri net. Concurrence and confliction mix in the Petri net system is called confusion, which is not a good property of a model，because it appears to be difficult to obtain a “correct” implementation when confusion emerges in the Petri net system, and for systems exhibiting confusion it is also difficult to analyze some properties in the Petri net system. Net theory suggests that it is not the combination of conflict and concurrence itself that causes difficulties in the Petri net system. Rather, it is those combinations of conflict and concurrence resulting in confusion that cause trouble. It is necessary to detect confusion and study some sub-net structure which might affect confusion. Based on the definition of elementary Petri net systems’ confusion, three kinds of basic structure of structural confusion are defined, which constitute a minimum-entirety-set of structural confusion. In this paper, some conclusions are proved: every structural confusion can be reduced to the basic structural confusion, and an algorithm detecting structural confusion and one method detecting three kinds of confusion are presented. This paper also motivates the need for illustrating the difference and affiliation between and with structural confusion and confusion in WF-net. It is shown that soundness is affected by its structural confusion with some examples.