The shortfin mako shark, Isurus oxyrinchus, is one of the most common bycatch species of the Taiwanese tuna longline fishery (Taiwan was second-largest shortfin mako shark-catching nation) in the Indian Ocean. The present study estimated the distribution and relative abundance indices of the shortfin mako in the Indian Ocean using observer records and logbook data from the period 2005–2018. To deal with the high number of zero catch records (∼90%), the catch per unit effort (CPUE) was standardized using a Zero inflated negative binomial model (ZINB). Cluster analysis was used to identify the fishing operations associated with different fishing strategies and then incorporated as a factor related to target species into the ZINB. Considerable variation was observed in the size distribution by region and season in the Indian ocean. Larger mako sharks (age>15 and age>7 yr for female and male, respectively) tend to occur in equatorial and tropical regions, while smaller specimens appear at higher latitudes in temperate waters. Cluster analysis produced five fishing clusters based on the catch compositions of the main species. The target factor (cluster) was important in explaining the variance in ZINB models. Overall, the standardized CPUEs and nominal CPUEs analysis for the shortfin mako caught by the Taiwanese longline fishery indicates a stable and increasing trend in recent years.