The Indian Ocean albacore (), which is widely distributed in the Indian Ocean from 25°N to 40°S, is one of the main target species of the Indian Ocean commercial tuna fishery. In recent years, China longline fleets have also targeted the albacore in the Indian Ocean. At present, several stock assessment models have been used to assess the Indian Ocean albacore tuna to determine the status of their stocks. However, there has been a substantial uncertainty regarding the results of these models. Therefore, in this paper, we have analyzed the factors influencing stock assessment for the Indian Ocean albacore tuna. This paper argues that:(1) substantial uncertainty exists in the catch and catch-at-size or catch-at-age data, because there were no, or incomplete, or incorrectly classified data from some important fleets reported, and the number of samples for size frequency data was very low, or the sampling protocols of the collection of size data changed with time; (2) although the catch per unit effort (CPUE) was standardized, the impacts of the changes in target species and the inhomogeneous distribution of fishing efforts of the fleets have still degraded the quality of the standardized CPUE; (3) because there were very few or limited studies on the biology of the Indian Ocean albacore, knowledge about their population structure, reproduction, growth, and natural mortality is limited, which has led to the values of some important biological parameters in the stock assessment models being set by using the results from the other oceans; (4) although the ocean environment has significant influences on the biomass dynamics and distribution of the Indian ocean albacore, only a few stock assessment models take these influences into account. These aforementioned issues have resulted in great uncertainties of the stock assessment. In the future, we need to further explore approaches to improve the quality of the stock assessment. However, at the same time, we have to develop a management strategy evaluation framework for the Indian Ocean albacore tuna to avoid the impacts of uncertainties of the stock assessment on the sustainable development of the fishery.