Global climate change has greatly increased the drought duration, frequency, and severity of intermittent river ephemeral stream (IRES), affecting the microbial-mediated biogeochemical process. While there is limited information about the responses of community structure and ecosystem functions of benthic biofilms in IRES, especially under the increased drought duration. Here, we focused on the increased drought duration and summarized their effects on the structure and functions of benthic biofilms in IRES. First, the increased dehydration duration led to distinct effects on the α-diversity or β-diversity of benthic microbial communities. The interaction network should be considered in future research as they are essential to maintain biofilm structure and play key roles in the resistance and resilience in biofilm community recovery under hydrological stress. In addition, inconsistent response patterns of the fundamental functions, such as gross primary production, ecosystem respiration, and functional enzymes activity of biofilms were discussed. Besides, the emissions of greenhouse gases (GHGs) of biofilms in IRES deserve more attention due to that their emission flux of biofilms could be significantly altered after prolong dehydration duration with a huge pulse when rewetting. More important, it is ecosystem multifunctionality rather than a single function that needs to be fully considered when studying the microbial functions and the biogeochemical process mediated by biofilms in IRES under increased dehydration duration. Also, more research is needed at larger spatial and longer temporal scales to evaluate the effects from a more macro perspective for better understanding the ecological impacts of increased dehydration duration in IRES ecosystems.