<p>To understand the effects of endophytic fungus Y118 on the physiological characteristics of <i>Zanthoxylum nitidum</i> (Roxb.) DC after co-culture with its host <i>Zanthoxylum nitidum</i>, we measured the plant growth index (dry root weight) of <i>Zanthoxylum nitidum</i> at different growth stages using the solid fermentation medium containing endophytic fungus Y118. Physiological and biochemical indexes (defensive enzyme activity) were determined by chromatographic analysis of the contents of nitidum chloride and chelidonine, the main active ingredients in <i>Zanthoxylum nitidum</i> root. At 3, 9 and 12 months, the root dry weight of the treatment group was 12.24, 1.56 and 1.47 times higher than that of the control group, respectively (<i>P</i> &lt; 0.01 or <i>P</i> &lt; 0.05). At 9 and 12 months, the peroxidase (POD) activity of the treatment group was increased significantly from the control group (<i>P</i> &lt; 0.05 or <i>P</i> &lt; 0.01). At 3, 6, 9 and 12 months, the phenylalanine ammonia-lyase (PAL) activity of the treatment group was significantly different from that of the control group (<i>P</i> &lt; 0.05 or <i>P</i> &lt; 0.01). At 12 months, chlorophyll a and chlorophyll b contents of the treatment group were markedly increased from the control group (<i>P</i> &lt; 0.05). At 6 and 9 months, nitidine chloride content in the treatment group was significantly increased from the control group (<i>P</i> &lt; 0.05 or <i>P</i> &lt; 0.01). At 9 months, chelidonine content in the treatment group was significantly increased from the control group (<i>P</i> &lt; 0.01). Inoculation with the endophytic fungus Y118 significantly improved the physiological tolerance of <i>Zanthoxylum nitidum</i> and promoted the growth of <i>Zanthoxylum nitidum</i>, thereby enhancing the quality of <i>Zanthoxylum nitidum</i>. This implicates Y118 as a potential artificial fertilizer for <i>Zanthoxylum nitidum</i>.</p>