In this study, we used the logbook data from the sampling vessels of the torch light fishery to distinguish the fishing grounds of bonito and Uroteuthis edulis and to standardize the catch per unit effort (CPUE) of U. edulis. The results showed that the fishing grounds where the sampling vessels targeted bonito from May to July were not the main distribution locations of U. edulis at that time. The monthly nominal CPUE of U. edulis showed two peaks when the bonito fishing effort was included and one peak when the bonito fishing effort was excluded. A generalized linear model (GLM) was used to standardize the nominal CPUE from 2009 to 2014. The GLM, which included the effects of year, area, fishing vessel, and month, as well as the interaction between area and month, explained 56.7% of the variation in the CPUE when the bonito fishing effort was included. The area had the main effect on the CPUE standardization. When the bonito fishing effort was excluded, the GLM including the same effects explained 47.7% of the variation in the CPUE, but the main effect came from the fishing vessel. The standardized CPUE trends based on the two data sets were similar and smoother than the nominal CPUE. The CPUE series showed that the abundance of U. edulis was the lowest in 2012 and peaked in 2013. Because of the difference of bonito and U. edulis fishing grounds, it is necessary to distinguish bonito fishing effort when calculating the CPUE of U. edulis.