Plant density significantly impacts photosynthesis, canopy structure, crop growth, and yield, thereby shaping the [CO ₂] fertilization effect and intricate physiological interactions in rice. An association panel of 171 rice genotypes was evaluated for physiological and yield-related traits, including the cumulative response index, under both normal planting density (NPD) and low planting density (LPD) conditions. LPD, serving as a proxy for elevated atmospheric [CO ₂], significantly increased all trait values, except for harvest index, compared to NPD. For the genome-wide association study, 386,817 high-quality SNPs were considered, employing both single-locus and multi-locus models, which collectively identified 172 QTNs, including 12 QTNs associated with at least two different traits under NPD or LPD conditions. A significant r­elationship between the percentage of favorable alleles in the genotypes and their performance under NPD and LPD conditions was observed. Potential haplotypes were validated using genotypes with contrasting [CO ₂] responses, grown under LPD and Free-Air CO ₂ Enrichment facility. These findings can enable efforts to selectively breed genotypes with favorable alleles and/or superior haplotypes for enhancing [CO ₂] responsiveness in rice. Climate smart rice varieties, with increased [CO ₂] responsiveness, have the potential to simultaneously enhance grain yield and quality while mitigating losses induced by high night temperatures.