The main purpose of this article is to apply the fuzzy analytic hierarchy process model to evaluate the key risk factors affecting cross-Strait shipping market for liner carriers. At first, according to the historical literature and experts’ opinions, a hierarchical structure with 4 risk aspects and 13 assessment criteria was constructed. Then, a fuzzy analytic hierarchy process algorithm model is proposed. Finally, based on the analytic hierarchy process experts’ questionnaires, we used the fuzzy analytic hierarchy process model to evaluate the key risk factors. The results show that (1) the "political risk" is the most important aspect affecting shipping market operations across the Taiwan Strait for liner carriers. (2) The top three critical risk factors are "shipping rate fluctuations and uncertainty," "political interference from local governments," and "discriminatory treatment and unfair competition," respectively. Furthermore, some recommendations concerning effective control and remedial measures addressing potential risk incidents are provided for liner carriers operating cross-Strait shipping market.