•We illuminate critical issues surrounding the collection and utilization of microclimate records in ecological studies.•Microclimatic responses to structural changes in ecosystems and landscapes have become a growing research focus.•Vapor pressure deficit is particularly emphasized for its applications in ecology.•We underscore the significance of microclimate in modeling major ecosystem processes. Drawing upon over 100 years of scholarly work on microclimate, we first present an overview of the history, key references, and critical issues surrounding the collection and utilization of microclimate records in ecosystem studies. We place particular emphasis on addressing specific and pressing issues related to the applications of microclimate at the community-ecosystem-landscape level, excluding those of controlled experiment such as growth chambers and greenhouses. Specifically, we: (1) highlight some key issues concerning the collection, quality assurance/quality control (QA/QC), and utilization of microclimatic data in ecosystem studies; (2) revisit microclimatic responses to the structural changes of ecosystems and landscapes; and (3) emphasize the significance of microclimate in understanding major ecosystem/landscape processes and functions. Vapor pressure deficit (VPD) is particularly emphasized for its calculation and use because of its burgeoning applications in the literature. Case studies for each of the three thematic topics are provided with selected references to demonstrate challenges and solutions. As the scientific community gears up to enhance microclimatic stations, we envision significant increases in the use of smart sensors, wireless access, networking, open databases, and computational capabilities. Understanding and addressing some of the issues raised in this synthesis paper may help advance microclimate research and foster collaboration with other relevant disciplines, such as ecosystem science.