The existence of endophytes significantly contributes to plant health and metabolism, however, the effects of endophytes on the volatile organic compounds (VOCs) metabolism of aromatic plant Cymbopogon citratus are still unclear. In this study, the endophytic bacteria from C. citratus grown at different seasons were isolated, and a dominant endophytic bacterium Bacillus sp. CcLf-2 was identified, with a fragrance-producing property. After seasonal analysis of the VOCs of C. citratus by headspace gas chromatography-mass spectrometry, found that the abundance pattern of CcLf-2 had a similar trend with the emission profile of citral, the primary and valuable composition of VOCs, in C. citratus. By inoculating CcLf-2 into C. citratus aseptic seedlings obtained by tissue culture, endophyte reisolation test verified the colonization of CcLf-2 in plants and the presence of CcLf-2, which can increased the citral proportion, obviously. Moreover, quantitative real-time PCR analysis of relevant genes in the citral biosynthesis pathway revealed that they were significantly up-regulated (at least P <0.05) with the existence of CcLf-2. The endophytic bacteria may enhance the citral production by modulating the expression of genes related to biosynthesis. And implies the possibility of using endophytic bacteria as a regulator to improving yields of some important VOCs in its host.