The design of an integrated coastal berths and entrance-channel system is a complex challenge, considering the stochastic environment and time-consuming calculation works. Therefore, the authors implement a decision support system (DSS) for designing integrated coastal berths and entrance-channel systems (ICBECS-DSS) by means of simulation and parallel computing. The ICBECS-DSS provides a three-dimensional (3D) integrated design environment with a broad set of fully integrated functions to evaluate the proposed design alternatives, and to identify an optimal design from a large number of alternatives. The key components of ICBECS-DSS are a process interaction-based simulation model for ship operation (PI-SMSO) and a Java parallel processing framework-based parallel computing program (JPPF-PCP). The PI-SMSO component simulates ships in and out of a one- or two-way traffic channel, or a one-way channel with a ships-passing anchorage along the channel (SPAC), and ships discharging/loading at berths. The JPPF-PCP component provides a parallel computing environment to reduce their processing time of running a large number of simulation experiments. Finally, the ICBECS-DSS is applied to a case study of a coal terminal, decides whether any expansion projects are needed, and proposes expansion strategies to improve its port performance. The results prove that the ICBECS-DSS performs well and is helpful for effectively designing berths and entrance channels together. Therefore, the ICBECS-DSS can be used for support in decision making in integrated berths and entrance-channel systems and provides a reference for government agencies involved with the design and operation of port systems.