Microplastic (MP) pollution in Antarctica is a hot topic that has gained increasing attention in recent years. However, information regarding MP pollution in Antarctic fishes is currently very limited. The present study provides the first evidence of the occurrence and characteristics of MPs in species from five families of the order Perciformes, from the Amundsen Sea (AS) and Ross Sea (RS), Antarctica. MP abundances within the order Perciformes were at a medium level on a global scale, but were higher than those reported in other Antarctic organisms. The detection rate and abundance of MPs in the order Perciformes from the RS (50% and 1.286 items individual−1) were both higher than those from the AS (36% and 1.227 items individual−1). Moreover, the major composition and size of MPs were, respectively, polyacrylamide (PAM) and 100–200 μm in the RS, but rayon and 500–1000 μm in the AS. These differences may be attributed to the different onshore scientific research stations, wastewater treatment facilities, marine activities, ocean currents, and local gyres in the two sea areas. Among the five fish families, members of the Artedidraconidae ingested the smallest MPs and the highest proportion of PAM, which is probably associated with their habitat and degradation effect of unique gut microbiome. The higher hazard index of MPs in fish from the RS is due to the presence of PAM and epoxy resin, which may also have far-reaching health implications for other Antarctic organisms and humans through food web transmission. Overall, long-term monitoring of MP pollution in Antarctic fish and their surrounding marine environment is highly desirable.