Seagrass is an important foundational species in marine ecosystems that plays an important role in providing ecosystem services. However, seagrass distribution and suitable habitat have rapidly declined in recent decades because of climate change and human-mediated disturbances. To achieved better conservation and management of the seagrass Zostera marina, an important representative seagrass in northern China, studies must investigate how this species responds to climate change. Here, we used an ensemble species distribution model to forecast the potential distribution and future suitable habitat change for the eelgrass Z. marina in coastal areas of the Bohai Sea and Shandong Peninsula, China. Two future climate scenarios, RCP 4.5 and RCP 8.5, were considered, which represent stable and high levels of greenhouse gas emissions, respectively. The ensemble model accurately predicted the current Z. marina distribution and performed better than the single-algorithm methods of random forest, generalized boosting model and maximum entropy according to performance matrices (AUC and TSS). The distance to land (78.50 ± 3.51%) and the maximum sea surface temperature (11.90 ± 0.25%) were the most important variables determining the distribution of Z. marina, while the contributions of other variables, maximum sea surface current velocity (3.80 ± 0.33%), minimum surface salinity (2.15 ± 0.22%) and water depth (1.74 ± 0.24%) were relatively low. Under future climate scenarios, the suitable habitat of Z. marina was predicted to decrease by more than half by the 2050s, whereas under the pessimistic greenhouse gas emission scenario (RCP 8.5), suitable Z. marina habitat was predicted to decrease by nearly 80% by the end of this century. The loss of Z. marina seagrass beds will have important ecological effects on the marine ecosystem. Our results not only provide valuable information to assist in identifying potential Z. marina meadows, but also have important implications for guiding conservation and management of Z. marina in the northern coastal region of China.