Given the minimum total time of vessel in port or minimum penalty cost as a functional objective, present berth-quay crane integrated scheduling model lacks fairness index of the service provided to vessels by the terminal. This phenomenon can affect the operating efficiency and the reasonable scheduling between terminal and vessel. This study proposed a multi-objective fair and continuous berth allocation algorithm, which considered vessel penalty cost, vessel waiting, and quay crane assignment. Specifically, The proposed algorithm considered the fairness index on berth allocation and designs the following three-stage procedure that maximizes service fairness: (1) computation of initial temperature, (2) neighbourhood searching to arrange for vessel berthing sequence and berthing location, and (3) assignment and adjustment of quay cranes to reach target low temperature. The proposed continuous berth allocation algorithm based on fairness maximization was comparatively verified with neighbourhood searching algorithm by combining different parameter strategies. Results show that the continuous berth allocation algorithm based on fairness maximization obtains the optimal solution within the time six times faster than the neighbourhood searching algorithm. Relevant conclusions provide a theoretical foundation for fairness study of the service in providing to vessels by the terminal.