The escalating demands of a growing global population and climate change require innovative strategies to enhance crop traits such as stress tolerance, nutritional value, climate resilience, and environmental adaptability, along with yield. Multi-omics technologies offer powerful insights into the molecular basis of these complex traits underlying molecular responses. High-throughput genotyping platforms ranging from next-generation sequencing (NGS) techniques such as whole-genome resequencing, transcriptomics, epigenomics, and QTL-seq to array-based tools, are accelerating gene discovery and trait mapping. The development of pan-genomes and comparative genomics tools enables the capture of hidden genetic diversity for broadening the genetic basis. Complemented by high-throughput phenotyping and envirotyping platforms, these innovations are fostering a systems-level approach to genomics-assisted breeding. Meta-omics approaches provide insights into plant–microbiome interactions in diverse environments, including the rhizosphere, phyllosphere, and endosphere. Metagenomics uncovers taxonomic diversity and functional gene pools; metatranscriptomics reveals active microbial gene expression under various field conditions while metaproteomics and metametabolomics shed light on functional protein networks and biochemical exchanges between microbes and rice. Integrating meta-omics with host genomics and phenotyping allows for a systems-level understanding of the rice holobiont. This review synthesizes recent advances in multi-omics and meta-omics applications for rice crop improvement, highlights key traits of interest, including yield, stress tolerance, nutrient-use efficiency, and their contribution toward Sustainable Development Goals.