The pelagic thresher shark, Alopias pelagicus, is a cosmopolitan species and abundant in Taiwan waters. The fishing season of pelagic thresher shark are from January to March in 1989-2017 off Taiwan waters. The annual landings of pelagic thresher shark ranged from 85.2 mt in 1994 to 328.7 mt in 2002, with a mean of 165.5 mt. The pelagic thresher shark catches were increasing from 1989 to 2005, however the mean weight of pelagic thresher shark individuals were decreasing in the time period. On the other hands, the catch decreased from 2006 to 2017, but the mean weight increased in the same period. The nominal CPUE were decreasing from 2005 to 2012, then increased to 2.31 (per thousand hooks) in 2014. The best-fitted general linear model selected by AIC and Chi-squared is Model 4: Zero-inflated with possion distribution. The standardized CPUE shows similar trends with nominal CPUE in 2005-2017.