The widespread occurrence and high bioavailability of microplastics have increasingly attracted wide attention of society. Because of the presence of microplastics in aquatic organisms, it is necessary to investigate their abundance in different species. Recently, the diversity of research methods for microplastics in aquatic organisms has resulted in different detection rates of microplastics; problematically, different results are poorly comparable. As a new global environmental problem, there is an urgent need to reach a consensus on the investigation and analysis methods involving microplastics. The formulation of standardized methods for microplastics in aquatic organisms is a scientific problem that needs to be resolved urgently in the research of microplastics. The current review systematically summarizes the recent progress in the extraction, separation, quantitative analysis and qualitative identification of microplastics in aquatic organisms. The advantages and disadvantages of the different methods are discussed. In addition, challenges faced by the development of standardized analytical methods for microplastics are discussed from the perspectives of the sampling representativeness of aquatic organisms, control of background values, analysis of nanoplastics, and application of identification technology. Further, the necessity and urgency of the standardization of analytical methods for microplastics are discussed.