Understanding the distribution pattern and its drivers of species is crucial for developing effective and sustainable management strategies. Amphioctopus fangsiao is the octopus of significant commercial and ecological value along the coast of China, with multiple distinct populations. However, research on their ecological dynamics remains limited and requires further investigation. Here, ensemble models were constructed to examine the spatio-temporal distribution and inter-populational differentiation in environmental adaptability of A. fangsiao in the East China Sea (ECS) and the South Yellow Sea (SYS). Specifically, we generated the ensemble models by integrating Gradient Boosting Machine (GBM), Generalized Linear Models (GLMs), and Maximum Entropy Models (MaxEnt) for the different populations across four seasons, using fishery-independent data collected from 2015 to 2021. The results revealed two hotspots of A. fangsiao in the ECS and SYS: one is the area of SYS along the coastal waters, with latitudes 33° N–34° N and longitudes 120° E–122° E (northern population, NP); the other one is near the Kuroshio-adjacent area with latitudes 28.5° N–29° N and longitudes 123° E–124.5° E (southern population, SP). Both NP and SP exhibited distinct seasonal habitat preferences, with key environmental drivers showing seasonal variations. The NP tended to inhabit coastal waters with lower sea surface heights (SSHs), shallower water depth, and a narrower sea bottom salinity range (SBS). In contrast, SP preferred marine environments with a thicker mixed layer thickness (MLT) and higher concentrations of bottom chlorophyll-a (Chl_b). The environmental characterization of suitable habitats revealed distinct patterns in resource utilization and environmental adaptation strategies between the two populations. This study provides fundamental data for understanding A. fangsiao population dynamics and underscores the importance of considering population-specific habitat preferences within dynamic marine environments.