Understanding the mechanisms that determine the critical habitat of commercial species is one of the significant challenges in marine science, particularly for species that inhabit the vast ocean worldwide. Previous investigations primarily focused on determining skipjack habitats without considering the feasible size for sustainable fisheries. To define habitat hotspots and movement patterns for decently sized skipjack tuna (≥50 cm) in Indonesia Fisheries Management Area (IFMA) 713, Indonesia, we examined the remote sensing of synoptic sea surface temperature (SST) and chlorophyll-a concentration (Chl-a) measurements with catch data from 2007 to 2016. A new skipjack tuna habitat model was developed based on the link between the key satellite-based environmental data and the best tuna fishery performance using a combination of generalized additive models (GAMs) and kernel density estimates. The findings reveal that feasible skipjack catch sizes were found in approximately 27% of total fishing grounds and were significantly captured in areas with a Chl-a of 0.15–0.28 mg m−3 and an SST of 29.5–31.0 °C, corresponding with an elevated skipjack habitat index (SHI). The habitat hotspots for the commercial skipjack were particularly produced by favorable Chl-a and SST, in association with Chl-a front and anticyclonic and cyclonic eddies, especially in October, which coincided with the highest skipjack catch per unit effort (CPUE). Skipjack distributions were mostly found within 10 km of favorable feeding habitats. They used the hotspot area as an indicator of their dynamics and movement pattern in the environment. The observed CPUEs cross-validated the predicted SHI values, suggesting that the model provided a reliable proxy for defining the potential habitats and the spatial movement of mature skipjack schools. Our findings have global significance for locating ecological hotspots, monitoring sustainable skipjack fisheries, and tracking skipjack migration, especially within the western tropical Pacific.