Increased atmospheric nitrogen (N) deposition generally promotes aboveground biomass in N-limiting terrestrial ecosystems, but the effects on underground carbon (C) processes and soil C sequestration remain controversial. This leads to considerable uncertainties in the evaluation of the C sequestration capacity caused by N deposition in terrestrial ecosystems. Atmospheric N deposition affects soil organic C (SOC) accumulation and depletion by directly changing microbial activity and/or indirectly changing substrate quality, and thereby changing the soil organic matter (SOM) decomposition. Previous research primarily focuses on soil C transformation processes and storage dynamics; however, limited information is available on the interaction among plants, microorganisms, and SOM, especially the biophysical and biochemical mechanisms involved in regulating plant-microorganism-SOM interactions with soil C sequestration. In this review, we summarize the effects of elevated N deposition on plant belowground C distribution, SOC priming effect, and microbial C metabolism, and analyzed the relationship between SOM chemical stability and microbial community dynamics. We identified a number of research topics which are in urgent needs of mechanistic investigation in the following decades:first, increased N input tends to reduce root growth and turnover, but the effects on C allocation in rhizosphere and associated mechanisms are unclear; second, although N availability can affect the direction and magnitude of the SOM priming effect, the contrasting effects of oxidized NO₃^- and reduced NH₄⁺ and the potential mechanisms on SOM priming effect are far from certain; third, microbial C use efficiency (CUE) is a crucial characterization of C metabolism of microbial communities, the bottleneck process for soil carbon emission. It is challenging to accurately quantify the microbial CUE and microbial turnover time owing to a lack of appropriate measurement methods; fourth, increased N input inhibits the activities of soil fungal communities and their extracellular enzymes, but the effects on the activity and composition of the soil bacterial community are inconsistent; moreover, the association between SOM chemical quality and soil microbial activity and composition is elusive. Therefore, we call for a long-term N control experiment platform to fully investigate the above-mentioned topics in a systems perspective. The most advanced techniques, such as stable C and oxygen isotopic tracer, organic matter chemistry, molecular biology, and macro genomics, will be used to analyze the belowground allocation of the plant-assimilated C, microbial C metabolism and turnover, and coupling between the SOM chemical structure and microbial functional groups. This long-term experiment could help understand the mechanism of plant-soil-microbial interaction and its contribution to SOC dynamics, improve the soil carbon models, and reduce the uncertainty of regional C sink assessment, and further lay a cornerstone for scientific managing terrestrial ecosystem in a changing world.