This dataset was collected from 31 surveys conducted between September 2021 and December 2022 in Chiku Lagoon, Taiwan, using locally adapted fishing methods (fyt nets). The surveys recorded 13,301 fish individuals, representing 55 families, 102 genera, and 145 species (155 taxa). The top five dominant species were Eubleekeria splendens (15.0%), Leiognathus equulus (11.1%), Planiliza macrolepis (8.5%), Nematalosa come (7.0%), and Pomadasys argenteus (6.9%). This dataset provides a comprehensive overview of fish species composition in Chiku Lagoon, offering critical baseline data for understanding fish biodiversity and supporting ecological studies in tropical and subtropical lagoons. Its detailed documentation of species diversity underscores the lagoon's ecological significance and its role as a vital habitat for various fish species.