Abstract Striped marlin (Tetrapturus audax) is an oceanic pelagic migratory fish. The stock status of striped marlin in the Indian Ocean is now considered to be overfished and subject to overfishing. Quantifying the level of at‐haulback mortality caused by longline fisheries for tuna and tuna‐like species is critical to reducing fishing pressure and protecting the fate of billfish stocks. This study was based on data from 2482 longline fishing operations recorded by Chinese observers in the western Indian Ocean from 2012 to 2019. The dataset includes information on the survival status of 774 striped marlin and their corresponding details. We used a generalized linear model (GLM) to analyse the level of at‐haulback mortality and its potential influencing factors. The results indicate that the distribution of 774 striped marlin had a lower jaw‐fork length (LJFL) range from 130 to 220 cm, and 51.5% of the specimens died at the time of haul‐back. The GLM model revealed that quarter, sea‐surface temperature (SST), hook type, LJFL, chlorophyll (CHL) and longitude had significant effects on at‐haulback condition when the fish were retrieved on board, with the quarter and sea surface temperature having the most significant effects. The interaction term between hook type and LJFL also had a significant effect on at‐haulback mortality, with the model predictions showing that mortality increased with LJFL when using circle hooks but decreased when using Japanese tuna hooks. There has been limited observational analysis of hooking mortality rates for striped marlin, and the present study may provide an important reference for the conservation and management of striped marlin stocks in the Indian Ocean.