Different fisheries, even the same fishery, use different ways of quantifying fishing efforts such as the number of vessels, days, voyages, and hooks. In squid-jigging fisheries, fishing hours, fishing days, and the number of vessels are valid units for calculating the catch per unit effort (CPUE). A vessel monitoring system (VMS) provides vessel position data with high spatial and temporal resolution and offers the possibility to quantify the CPUE at a finer scale. Using the squid fishery in the equatorial waters of the eastern Pacific as a case study, the CPUE was evaluated and standardized based on VMS data. The drifting operating points of the squid fishing vessels were filtered by the speed threshold, solar radiation, and operating time setting methods, leading to the number of fishing hours per day, and the nominal CPUE was calculated by combining the catch data obtained from logbooks. Then, the generalized linear model (GLM) and generalized additive model (GAM) were applied to conduct CPUE standardization considering spatiotemporal factors and environmental variables including sea surface temperature (SST), sea surface salinity (SSS), sea surface height (SSH), and chlorophyll-a (Chl_a). The results showed that month, latitude, SST, SSH, and Chl-a all have a high significant effect on CPUE as demonstrated through the significance test conducted by GLM. The GAM including the significant factors was judged to be the best model according to the AIC guidelines. The latitude range for high CPUE in the fishery was 3°S~0°S, SST range 24~25 °C, SSH range 4~8 m, and Chl_a range 0.15~0.20 mg/m3. In addition, the nominal and standardized CPUEs were compared based on fishing hours and fishing days. The results indicated that the two types of CPUEs were highly related hence there was no significant difference.