The sandy Pinus sylvestris var. mongolica plantation that as the boundary part of the Three North Shelterbelt Project in Northeast China has been well protected and prohibited disturbance more than ten years, and thus bring about lots of forest floor litter and then humus layer. While humus layer accumulation that could change the interface between litter and soil, its effects on litter and soil, and especially the interaction among them were still poorly understood. Hence, three different treatments that included remove all forest floor litter and humus, double forest floor litter and humus layer, and retain forest floor litter and humus original (no treatment) were conducted, and the physicochemistry properties and microbial communities were monitored. Results showed that the humus layer increased forest floor litter decomposition rate and its total carbon, total nitrogen and total phosphorus significantly, while it changed soil pH and nutrients differently and slightly. The abundances of bacterial groups at different taxonomic levels increased and while its diversity indexes decreased in litter when the humus layer existed, however, the fungi community both in litter and soil varied insignificantly. The humus layer not only increased remarkably the proportions of common OTUs between humus and litter, humus and soil compared to litter and soil both for fungi and bacteria, but also decreased the differences of the number of fungal and bacterial taxa statistics between litter and soil. It implied that the humus layer could act an important role in the recover process of degraded forest ecosystem.