The phenomena of allelopathy were realized since ancient times in agricultural production. Allelochemicals from rice are secreted in the rhizosphere and suppress the growth of weeds. The process of allelopathy is regulated by many genes such as those signaling the synthesis and metabolism of allelochemicals by the plant. Identification of genes that regulate rice allelopathy is crucial to an understanding of the mechanisms of allelopathy in rice. In this study, the allelopathic cultivar PI312777 was selected for evaluation using gene chip technology and bio-informatics to analyze and select the relative genes in regulaion of rice allelopathy according to reported types of allelochemicals. Expression vectors were then constructed and transferred into rice by agrobacterium-mediated transformation for functional verification. The results showed that there were around 40 genes closely related to the stress conditions, and 10 genes related to synthesis and metabolism of phenolics. Bio-informatics analysis of gene chip data indicated that the pathways elicited under stress conditions were quite different for PI312777 and Lemont. Phenylpropanoid biosynthesis was the main pathway for PI312777, while carbon fixation was key for Lemont. C4H (Os05g0320700 or CYP73A38) was one of the key genes. The effects of transgenetic rice and PI312777 on the growth of barnyardgrass were similar, and 5 phenolic compounds were also detected by HPLC to identify the selected gene functions. The results proved that allelopathic potential could be improved by increasing gene expression, and phenolics were the most important chemicals in rice allelopathy. These results provided not only new evidence for understanding the molecular mechanism of regulating rice allelopathy, but also a clue for obtaining genes for improvement allelopathic potenial in modern rice molecular breeding.