The Spanish mackerel (Scomberomorus niphonius) is widely distributed in the China Seas. It is a commercially important marine fish species, which has maintained a high yield in China for many years. With the recent decline in fishery resources, S. niphonius has played an increasingly important role in Chinese capture fisheries. Therefore, it is of great significance to analyze the status of fishery resources for the sustainable utilization and rational management of S. niphonius. Catch per unit effort (CPUE), commonly used as an index of the relative abundance of fish populations, is one of the most important data sets used for fishery stock assessment. Fishery-dependent monitoring programs are a common source for collecting data for stock assessment and fishery management, as it is more cost-effective and may collect data on a larger spatio-temporal scale compared with that of fishery-independent survey programs. However, the nominal CPUE calculated based on the fishery-dependent survey data is usually influenced greatly by various factors, such as temporal (e.g., year and month), spatial (e.g., longitude and latitude), and environmental (e.g., sea surface temperature) factors. It is essential to standardize the CPUE before it is used in fishery stock assessment. Generalized additive models (GAM) are commonly applied to standardize CPUE data. Based on the logbook data of monitoring fishing vessels in Shandong Province in 2012–2018, the CPUE and variations in the barycenter of fishing grounds for S. niphonius pair trawler fishery in the Yellow and Bohai Seas were studied. The GAM model was used to analyze the relationship between the nominal CPUE of S. niphonius and the spatio-temporal and environmental factors, such as sea surface temperature, and to standardize the CPUE. The results showed that the nominal CPUE and barycenter of the fishing grounds of S. niphonius had clear monthly and annual changes; the nominal CPUE showed a fluctuating downward trend from 2012 to 2018, and the maximum appeared from September to November each year. The monthly changes in the barycenter of the fishing grounds included a spatial shift from the southeast to the northwest and then to the southeast throughout the year, which was consistent with the migration patterns of S. niphonius. The barycenter of the fishing grounds showed yearly variation, and the variation in longitude was opposite to the trend of sea surface temperature change, whereas the variation in latitude was the same as the trend of sea surface temperature change. The results of the GAM model showed that year, sea surface temperature, longitude, and latitude had an extremely significant effect on nominal CPUE, among which the year had the most significant effect on nominal CPUE. The nominal CPUE showed an increasing trend with sea surface temperature. The standardized and nominal CPUEs had similar variation trends, but the fluctuation range of the standardized CPUE was small, and its value was lower than that of the nominal CPUE.