Nitrogen dynamics at ecosystem levels profoundly impact the Earth’s surface system due to their environmental and ecological significance. Exploring the sources and transformation of nitrogen in various Critical Zones is vital to understanding biogeochemical cycles and sustainable development. This study summarized nitrogen characteristics in soil profiles and nitrogen dynamics in diverse terrestrial ecosystems based on data from typical Critical Zones of China. The results indicated that nitrogen accumulates in the deep soils of cropland ecosystems due to intensive fertilizer applications, which potentially harms soil functions and water quality. Therefore, it is necessary and meaningful to take adequate measures to alleviate nitrogen accumulation in deep soils. Additionally, surplus nitrogen transported into groundwater and riverine systems from soil has emerged as an important issue for environmental management. There are serious nitrogen pollution issues in many river water and groundwater areas, which could be addressed by reducing the fast leaching and considerable nitrogen accumulation in the vadose zone. Systematic and long-term observational studies are needed to achieve the ultimate goal of ecological conservation and high-quality development. Therefore, future research should consider monitoring and evaluating ecosystems based on the long-term Critical Zone Observatories networks to advance appropriate environmental management strategies that adapt to nature’s rules and strengthen the ecosystem service function for sustainable development.