The pelagic cephalopod species jumbo flying squid Dosidicus gigas is ecologically and economically important in the Humboldt ecosystem off Peru. This squid species is sensitive to oceanic environmental changes, and regional oceanographical variability is one of the important factors driving its redistribution. Off Peruvian waters, mesoscale eddies are ubiquitous and dominate the biogeochemical processes in this region. This study first explored the role of mesoscale eddies in regulating the environments and their effects on the abundance and habitat distribution of D. gigas off Peru by analyzing squid distribution in eddy-centric coordinates and building a habitat suitability index (HSI) model. Results indicated that the abundance and habitat distribution of D. gigas in mesoscale eddies varied across months, with significant differences observed between anticyclonic eddies (AE) and cyclonic eddies (CE). In AE, a higher abundance and proportion of suitable habitat occurred. While in CE, the abundance was relatively low and the suitable habitat was relatively less, concentrating at the periphery of CE. Based on the HSI model results, sea surface temperature (SST) and 50 m water temperature (T50m) in AE were more favorable for D. gigas, which was 0.3-0.5 °C lower than that in CE, yielding high-quality habitats and higher abundance of D. gigas. Our findings emphasized that mesoscale eddies have a significant impact on water temperature conditions and nutrient concentrations off Peruvian waters.