An ecosystem can provide multiple functions and services at the same time, i.e., ecosystem multifunctionality (EMF). Above- and belowground biodiversity and abiotic factors have different effects on EMF. Human activities increase atmospheric nitrogen (N) and phosphorus (P) deposition, but the mechanism of how atmospheric N and P deposition affect EMF in alpine meadows on the Tibetan Plateau is still unclear. Here, we measured eleven ecosystem parameters to quantify EMF by averaging method and explored the impact of plant and microbial species diversity and abiotic factors on EMF after long-term field N and P addition in alpine meadows on the Tibetan Plateau. Results showed that N addition reduced EMF by 15%, NP increased EMF by 20%, and there was no change due to P addition. N and P addition reduced pH, relative light conditions (RLC), and plant species richness and modified plant and fungal community composition. Structural equation model (SEM) analysis confirmed that fungal community composition was an important and positive driver on EMF. These results provided an understanding of how N and P addition affect EMF directly and indirectly through biotic and abiotic pathways, which was important for predicting the response of EMF to atmospheric N and P deposition in the future. Furthermore, the findings suggested that soil fungal composition was more important driving factors than abiotic factors in the response of EMF to N and P addition and the importance of the interactions between plant and soil microbial species diversity in supporting greater EMF.