As a result of the increasing global production and usage of plastics, a large amount of microplastics has been widely detected in many environmental media, especially in the aquatic environment, causing environmental risks. Autotrophic organisms including phytoplankton, aquatic plants and some autotrophic microorganisms are the main primary producer in lake ecosystems, and are the key components of the lake food chain, providing energy and material base for upstream of the food chain. In addition, as the main primary producers in freshwater, phytoplankton is the most sensitive component and respond fast to environmental changes. Therefore, phytoplankton was used as indicator for assessing the status of lake ecosystem function and stability. Understanding the response of phytoplankton to microplastics is crucial for clarifying the effect of microplastics on lake ecosystem functioning. Here, we summarized the distribution characteristics (abundance, type, and size) and source of microplastics in global lake ecosystems, and systematically analyzed the effects and the involved mechanisms of microplastics exposure on the cellular structure, gene expression and growth, as well as the content of Chlorophyll a and photosynthetic activity of phytoplankton and other aquatic organisms. In summary, the microplastics could inhibit the chlorophyll a content and photosynthetic activity of the primary producers. The higher the dose and the smaller the size, the stronger the inhibitory effect of microplastics. Microplastics could cause cell membrane damage, DNA damage, regulate the functional gene expression, and inhibit the growth of the primary producers, simultaneously. The impact of microplastics on primary producers in lakes could subsequently lead to an impact on lake function. However, the actual level of microplastic concentrations in lake ecosystem was much lower than the dose of additives in the incubation experiment in lab, and the structure and components of microplastics in lake are more complex than that in the incubation system in lab. Thus, the direct correspondence between field investigation and indoor incubation experiment could not be built yet. Therefore, future research should conduct incubation studies with microplastics that are closer to the environmental concentrations and compositional characteristics in lake ecosystem, and focus on how to build an efficient linkage of the results obtained in field investigation and indoor incubation experiment. A reliable and universal dose-effect relationship model between microplastic concentrations and the primary producers should be established to explore the mechanism of microplastics impact on lake primary producer and productivity, as well as provide scientific support for clarifying the mechanism of microplastics impact on lake ecosystem functioning.