Microplastics (MPs, <5mm in size) have rapidly spread across aquatic ecosystems, which urgently needs systematic assessment for their ecological risk. Fish species have frequently been selected as indicator organisms in evaluating MPs contaminants. However, it has been questioned that which organs of fishes should be examined due to tissue-specific results. In this study, we investigated the accumulation and depuration process of MPs in the main organs of zebrafish under different MPs concentrations as well as the presence and absence of food resources. Our results recorded consistently higher MPs accumulation in fish guts among different MPs concentrations, implying fish guts as stable organs representing organisms’ MPs contaminants. Meanwhile, MPs accumulated in fish guts increased significantly with increasing exposure concentrations, highlighting fish guts as sensitive organs in reflecting MPs contamination in aquatic environments. In addition, MPs accumulated in fish guts under non-feeding conditions followed a logistic “S” curve while fluctuated under feeding conditions, suggesting increased ecological MPs risk with the absence of food resources. The depuration rate in fish guts was significantly higher in the feeding group than in the non-feeding group, implying better expelling ability of MPs with the presence of food resources. Our study proposes fish guts as the optimal indicator organs in assessing the ecological risk of MPs contaminants in both fish bodies and aquatic environments, and highlights the importance of sustaining sufficient food resources in aquatic environments to reduce the MPs triggered adverse effects on fish species.