Based on commercial fishing data (Catch per unit effort, CPUE) from June to September selected from 2003 to 2012 (without the data of 2005), this study aims to explore the spatial structure of D. gigas resources and reveal the correlated environmental factors. To reach the research goals, the methods of geo-statistics were used, including global and local spatial auto-correlation, and semi-variogram. Classical statistics and global spatial autocorrelation showed that there was medium degree of aggregation over the study area. Relatively strong aggregated distributions were observed for Dosidicus gigas in the high sea off Peru in June. Additionally, trend analysis demonstrated that there were more squids distributed in the northern areas than those in the southern. However, there are more squids in the middle than those at the both ends in longitude direction. According to determination coefficient (R²) and residual sum of squares (RSS), Gaussian models were fitted in June and August, spherical model fitted in July, and exponential model was fitted in September. Moreover, nugget coefficients were 41.33%,24.66%,25.89% and 35.42% from June to September, respectively, and whose implications of aggregation for distribution were consistent with global auto-correlation. Finally, the correlation analysis between CPUE and environmental factors revealed the reason of spatial heterogeneity of D. gigas in the high sea off Peru from June to September. The environmental factors included sea surface temperature (SST), sea surface salinity (SSS), sea surface height (SSH) and chlorophyll-a (Chl.a). And this study suggested SSH was the most influential among those four factors. However, the mechanism of how SSH affects the distribution of D. gigas was not investigated in this study. All in all, it is important for habitat distribution and ecological study to analyze this species distribution and its spatial heterogeneity.