A 2-D unstructured finite element model is used to study how local and remote atmospheric forcing, sea level rise, and shoreline variation affect typhoon-induced storm surge in a small shallow bay, Zhanjiang Harbor (ZH). In this research, the spatial distribution of storm surge is divided into three patterns in ZH, denoted E-W, N-S, and S-N, using a quantitative method. In the Bay, local atmospheric effects (LAE) and remote atmospheric effects (RAE) both play important roles in the maximum residual water level. The contribution of RAE to the inflow is higher than that of the LAE, but the former is less important in the spatial distribution in ZH. In addition, the typhoon track influences the time of occurrence of the maximum surge by forcing the outer waters to ZH, then the spatial distribution of the surge residual in the bay is controlled by local winds, and different regions are threatened during different kinds of storm surge processes. Two sea level rise scenarios are set up in the paper as well, and the results show that the trends of the changes in LAE and RAE in the inner-bay are the opposite in the case of sea level rise; however, the total changes of the distribution are not the same in different categories. In general, the E-W category storm surge is weakened, while the N-S and S-N category storm surges have inverse changes in the north and south of ZH. There is a downward trend of the maximum surge gradient within the Bay, but relative to sea level rise itself this effect is not obvious. The establishment of the sea embankment increased the storm surge within the bay though it is not significant.