Species distribution models (SDMs) are used to detect potential effects of climate change on the habitat suitability of macrobenthos in the Yellow Sea and East China Sea. We obtained the presence/absence data of five dominant and characteristic macrobenthos from 268 sites investigated during 2000–2016 and 13 environmental variables from online datasets. The ensemble SDMs were constructed and were in good model performance for all five species. Model projections showed that the five species displayed different reactions to future climate scenarios: two species (the ophiuroid Ophiura sarsii vadicola and the bivalve Thyasira tokunagai) will likely contract their ranges, two (the crab Xenophthalmus pinnotheroides and the polychaete Sternaspis chinensis) will likely expand their ranges, and one (the ophiuroid Amphioplus japonicus) will likely move northward. Those differences were mainly due to their difference in thermal tolerance. Our findings provide important scientific basis for understanding the influence of climate change on marine benthic ecosystems.