Forest ecosystems play important functional roles over a broad spatial scale in our environment ranging from biodiversity sustainability and ecosystem services at local scales to carbon and water cycles at local, regional and global scales. Micrometeorological observations, ecological research, remote sensing, and simulation models have been used to reveal the dynamics of CO2 exchange between the atmosphere and forest ecosystems, as well as ecological and biogeochemical processes of the carbon cycle in such ecosystems in a changing environment. However, as the structure and functions of forest ecosystems in a mountainous landscape are characterized by their spatial heterogeneity due to the topographic and climatic conditions, ecosystem science needs to develop a multidisciplinary approach. In addition to these carbon cycle between the atmosphere and ecosystems, biogeochemical and hydrological cycles at forested catchments (basin ecosystems particularly in a mountainous landscape) should be explored to clarify and evaluate the ecosystem functions and services under climate change and human impacts. The following are reviewed: (1) long-term and multidisciplinary researches on forest ecosystem structure and functions in a cool-temperate deciduous forest by applying micrometeorological observations, ecological research, plant photosynthesis modeling, and in-situ and satellite remote sensing, (2) challenges of research topics and opportunities involving forest and catchment ecosystems in a mountainous landscape for revealing the dynamics of biogeochemical cycles in changing environments, and (3) our expectations to addressing these scientific challenges by networking research networks from different disciplines.