In this study, we collected and analyzed the landing data of the gillnet fisheries collected by port enumerators in 12 fishing harbors of the Tainan city, Kaohsiung city and Pingtung county during the period of January 2015 to December 2019. We tried to investigate the fishery status, composition of the landings, fishing seasons, alteration index and migration index of the gillnet fisheries to understand the structure of fishery resources in the offshore waters in the southwestern waters of Taiwan. The result indicated that there were 435 active fishing boats among the 3 cities in 2019. In Tainan (TN), the landings were mainly came from CT2 and CTR fishing boats. In Kaohsiung (KH), it mainly came from CTS boats. In Pingtung (PT), all the landing came from CTR boats. The average fishing days were 88, 96 and 83 day per year for TN, KH and PT, respectively. The summer months (from June to August) were the low season for the gillnet fisheries, while the peak season were between October to next February during the winter. The top 5 dominant taxa comprised 37.1%, 57.4% and 70% of the total catch in TN, KH, and PT, respectively. On the other hand, the diversity index was highest TN and lowest in PT. In general, the variation in the composition of fishes was significant in TN and PT, and was relatively stable in KH. The seasonality of the dominant fishes was evident in TN and PT. By contrast, the seasonality was not obvious. The alteration index indicated that the composition of fishes was most stable during winter, followed by the autumn, and was most unstable during spring and summer in the southwestern waters of Taiwan. Similarly, the migration index revealed that the composition was most stable during winter. The migration of fishes off TN was most evident during spring and was most evident during summer for KH and PT. During autumn, after the low season of summer, the fish stocks moved in and migrated toward each county.