With increasing global demand for deep-sea resources, polymetallic nodule mining has become a potential approach for accessing critical minerals. To identify potential areas of ecological concern associated with future deep-sea mining activities, this study predicted the suitable habitat distribution of Balaenoptera species in the Pacific polymetallic nodule areas using the Maximum Entropy Model (MaxEnt). The results showed that environmental variables, such as temperature, salinity, and chlorophyll-a concentration, were the major contributors to Balaenoptera habitat suitability, with their combined contribution exceeding 70% across four species. Temperature showed the highest contribution to habitat suitability predictions for B. acutorostrata, B. edeni, and B. physalus, with contribution values of 38.2%, 46.4%, and 45.4%, respectively. In contrast, salinity contributed the highest (38.4%) to the habitat suitability of B. musculus. Moreover, future climate scenarios posed different changes in the predicted suitable habitats for different Balaenoptera species. Under the current climate scenario, a large proportion of suitable habitat (PSH) were affected in the eastern Pacific mining areas, including 8.52% for B. acutorostrata, 54.94% for B. edeni, 53.73% for B. musculus, and 20.74% for B. physalus. Under future climate scenarios, the PSH of B. acutorostrata and B. musculus showed an increasing trend, which was especially pronounced under the SSP1-2.6 climate scenario (3.96% and 17.27% respectively); while B. edeni showed opposite trends, with a decrease (−6.14%) under SSP1-2.6 and an increase (4.91%) under SSP5-8.5 scenario. The PSH of B. physalus showed a slight decrease (−0.43% and −0.32%) under both scenarios. These findings may support future environmental management and impact assessment for deep-sea polymetallic nodule exploitation.