Abstract: Freshwater benthic algae are important components of aquatic ecosystems, and their species diversity and ecological functions are crucial for maintaining the health of the water environment. However, in recent years, the combined influence of human activities and climate warming has led to abnormal proliferation of certain benthic algae (such as toxin-producing filamentous cyanobacteria and proliferating green algae with coverage characteristics), triggering chain ecological problems such as water quality degradation and impairment of ecosystem service functions. This study applies bibliometric methods to quantitatively analyze freshwater benthic algae research published over the past six decades. This paper first provides an overview of benthic algae diversity and habitat characteristics, elaborating on the ecological functions of benthic algae in the environment and the potential ecological risks associated with their excessive proliferation. It then systematically reviews the external factors and mechanisms affecting the benthic algae growth, including abiotic factors (water temperature, thermal stratification, water level fluctuations, light, and nutrients) and biotic factors (such as grazing effects). Finally, based on the current state of knowledge, future research directions are proposed to provide references and entry points for current studies on freshwater benthic algae.