Exogenous jasmonic acid (JA) and salicylic acid (SA) can have an important effect on rice allelopathy. Currently, the role of endogenous JA and SA on rice-barnyard grass interaction is largely unknown. In this study, the levels of JA and SA in tissues and their correlation to rice allelochemicals inducing with barnyard grass are analyzed. Rice allelochemicals production was enhanced by coexistence with barnyard grass and allelochemicals of the allelopathic variety, PI312777 were generally higher than those of non-allelopathic variety, Liaojing9. Furthermore, JA contents of two rice varieties were generally greater in roots than in shoots, and differed clearly with tested times. The SA levels of PI312777 were generally higher than those of Liaojing9 in shoots but opposite trend in roots. The contents of total allelochemicals correlated positively with SA (Pearson correlation, r = 0.91, P < 0.001). These results indicate that as the phytohormones, JA and SA play a provable role in chemical communication between rice and barnyard grass and participate in rice-barnyard grass allelopathic interaction. Future studies should determine the signal molecules in root exudates of barnyard grass and their functions.