Liaodong Bay is one of the largest semi-enclosed bays located in Bohai Sea, in northeast China. It is an important feeding and spawning place, even wintering and breeding migration base for many marine organisms. The size structure of phytoplankton communities is a key feature of marine ecosystems and can be used as an indicator for algae disaster, but the methods to evalute is still challenging. Here, we compared the size-fractionated chlorophyll- a method with a high-throughout sequencing method in an evaluation of the size structure of phytoplankton assemblages in Liaodong Bay, China, in 2014. The proportion of picophytoplankton was estimated at just 19% according to the results based on size-fractionated chlorophyll- a, which likely represents a severe underestimation. The sequencing method confirmed that many kinds of phytoplankton species appeared in more than one size-fractionated filter membrane, with some even dominating where the filter membrane pore size was greater than the individual phytoplankton size. According to the sequencing method, the phytoplankton assemblages in Liaodong Bay were dominated by picophytoplankton (average proportion = 44%), followed by the nanophytoplankton (average 32%), a composition that is more consistent with other studies. The sequencing method provides a more robust way to assess the size structure and taxonomic diversity of marine phytoplankton communities.