Protocol-level mismatch is one of the most important problems in service composition. The commonly used reachability exploration method focuses on verifying deadlock-freeness. When this property is violated, the states and traces in the reachability graph only give clues to re-design the composition. The process must then repeat itself until no deadlock is found. In this paper, multiple web service interaction is modeled with a Petri net called Composition net (C-net). The protocol-level mismatch problem is transformed into the deadlock structure problem of a C-net. If mismatches are found, a solution based on Petri net siphons is proposed. The proposed method is shown to achieve higher efficiency for resolving protocol-level mismatching issues than traditional ones do.