Plant-microbe interactions play a crucial role in enhancing plant growth, nutrient uptake, and resilience to environmental challenges. In rice cultivation, understanding these intricate dynamics is essential for developing sustainable agricultural practices. Meta-omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, provide powerful tools to study the complex relationships between rice plants and their associated microbial communities. This chapter examines the application of these integrative approaches to elucidate the molecular pathways governing plant-microbe interactions, emphasizing their roles in nutrient cycling, pathogen suppression, and stress mitigation. It further highlights recent progress in harnessing meta-omics data to identify functional traits and develop microbial consortia beneficial to enhance rice productivity. Additionally, challenges associated with data integration, interpretation, and translation into field applications are discussed. By elucidating the molecular intricacies of plant-microbe dynamics, this chapter underscores the potential of multi-omics-driven strategies in fostering sustainable rice production while addressing global food security and environmental sustainability.