Root-knot nematode, among the most destructive plant-parasitic nematodes, poses a severe threat to global agricultural production. The plant root microbiome is considered as the “second genome” of host plant and plays an indispensable role in plant growth, development, and stress response. Parasitism by root-knot nematode significantly disrupts the community structure and function of root-associated microbial communities in plants. The disturbance of host microbiome not only exacerbates plant pathological processes but also may induce cascade effects through tripartite interactions among microorganism, plant, and nematode. This review comprehensively elucidates the multifaceted impacts of root-knot nematode parasitism on the root micro-ecosystem of host plant, particularly focusing on the variation in the structural and functional characteristics of both the rhizosphere and endophytic microbiome, as well as their roles in the occurrence of nematode diseases and maintaining plant health. Investigating the interaction between pathogenic nematodes and plant microbiome on community level will not only advance our understanding the intricate network among plant, nematode, and microorganism, but also provide theoretical and practical insights for developing innovative strategies for controlling plant nematode diseases.