Container liner shipping is a kind of transportation mode that is operated according to a schedule. Although the goal is to operate container liner ships on time, the actual arrival time and handling time often deviate from the schedule due to uncertain factors. The identification of a proper probability distribution to describe time deviation law will have a significant impact on accurately recognizing the uncertainty of the operation of container liner ships. In view of this problem, this paper discusses the basic characteristics of container liner ships’ operation time, analyses the properties of relevant probability distributions, and selects representative container ports around the world to collect data on the container liner ships’ operation time for statistical verification. The results show that under schedule constraints and interference uncertainty, the time deviation presents a specific state between a fixed length and random distribution that conforms to the properties of an Erlang distribution. Given that container liner shipping follows the same operation rules worldwide, it is reasonable to deduce that the time deviation law could be generalized to other container ports. Finally, the practical value of this study is demonstrated through quantitative evaluation of port congestion degree under various probabilistic models.