To solve the issues of low survival rate and poor vigor of Zanthoxylum bungeanum seedlings caused by long-term continuous cropping, a study was conducted using bio-organic fertilizer and microbial bacterial fertilizer as repair agents. The aim was to investigate their effects on the physiological metabolism of Zanthoxylum bungeanum seedlings and soil phenolic acids, with a focus on understanding the growth-promoting mechanism of replanted Zanthoxylum bungeanum. The results revealed that fertilization significantly increased the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), nitrate reductase (NR), as well as the levels of soluble sugar (SS) and soluble protein (SP) in Zanthoxylum bungeanum seedlings. Conversely, the content of malondialdehyde (MDA) and four soil phenolic acids (gallic acid (FA), ferulic acid (GA), caffeic acid (CA), and p-hydroxybenzoic acid (PHBA) were significantly reduced. The mixed application of microbial fertilizer and bio-organic fertilizer showed better growth-promoting effects compared to single application. Specifically, when the volume ratio of microbial fertilizer and bio-organic fertilizer was 2:1, the activity of defense enzymes was most significantly promoted. Under this treatment, the activities of SOD, CAT, POD, and NR in seedlings were 1.8, 3, 3.8, and 5.3 times higher than the control (no fertilization treatment), respectively. The levels of SS and SP were 2.4 and 2.5 times higher than the control, respectively. The MDA content was 27% of the control, and the total content of the four phenolic acids was 60% of the control. Principal component analysis results showed that the scores of fertilization treatments were higher than the control, with the order being T6 > T7 > T2 > T5 > T4 > T3 > T1 > T0. Therefore, the combined application of microbial fertilizer and bio-organic fertilizer effectively promotes the physiological metabolism of seedlings, reduces the content of soil phenolic acids, and has a positive effect on alleviating the obstacles to continuous cropping of Zanthoxylum bungeanum.