Nitrogen addition affects plant-arbuscular mycorrhizal fungi (AMF) association greatly. However, although the direct effect of nitrogen addition on AMF colonization has received investigation, its indirect effect through shifts in plant community composition has never been quantified. Based on a 7-year nitrogen addition experiment in an alpine meadow of Qinghai-Tibetan Plateau, we investigated the effects of nitrogen addition on both plant community, AMF diversity and colonization, and disentangled the direct and indirect effects of nitrogen addition on community AMF colonization. At plant species level, nitrogen addition significantly decreased root colonization rate and altered AMF community composition, but with no significant effect on AMF richness. At plant community level, plant species richness and AMF colonization rate decreased with nitrogen addition. Plant species increasing in abundance after nitrogen addition were those with higher AMF colonization rates in natural conditions, resulting in an increased indirect effect induced by alternation in plant community composition with nitrogen addition, whereas the direct effect was negative and decreased with nitrogen addition. Overall, we illustrated the effect of nitrogen addition and plant species in influencing the AMF diversity, and demonstrated how shifts in plant community composition (indirect effect) weakened the negative direct effect of nitrogen addition on community-level AMF colonization rate, and emphasized the importance of plant community-mediated mechanisms in regulating ecosystem functions.