Plant–endophytic fungi are widely distributed and highly diverse, with many of them capable of influencing plant growth and development, which is related to the production of volatile organic compounds (VOCs). While certain fungal VOCs have been found to stimulate plant growth, others exhibit inhibitory effects. Importantly, the impact of fungal VOCs extends beyond host plants to affect non-host plants as well. In this study, we isolated two plant–endophytic fungi, Clonostachys sp. CC1 and Clonostachys sp. CC2, from healthy rice roots. These strains were co-cultured with both rice and Arabidopsis thaliana. Our results demonstrated that both strains significantly enhanced the growth of both rice and A. thaliana. Specifically, they increased the length and biomass of rice and A. thaliana seedlings, as well as the chlorophyll content, while decreasing the H₂O₂ content in the leaves of both plants. The VOCs produced by these strains were analyzed using gas chromatography–mass spectrometry (GC-MS), which identified a total of 10 main ingredients. Among these compounds, 1-pentanol, ethylbenzene, and dimethyl phthalate inhibited the growth of rice while promoting the growth of A. thaliana, highlighting the variability in the effects of these compounds on different plant species and the complexity of plant–fungal interactions.