Abstract: In order to investigate the effect of cake fertilizer on the rhizosphere colonization of Bacillus and the growth promotion impact of colonized Bacillus on tobacco seedlings, Bacillus amylolyticus HZ13 (P1), cake fertilizer (P2), instantaneous mixture of cake fertilizer and HZ13 (P3), and co-fermentation culture of cake fertilizer and HZ13 (P4) were added to tobacco seedling soil respectively, and soil without any additives served as the control (CK). The rhizosphere metabolites of tobacco seedlings in each treatment were extracted and the different metabolites between treatments were analyzed. The chemotaxis of HZ13-RFP, the number of rhizosphere microorganisms and the growth index of tobacco seedlings under different treatments were compared. The results showed that P4 rhizosphere had the most metabolites and organic acids. There were 20 differential metabolites between P4 and CK, mainly organic acids and saccharides, with glucose and maltose being the most abundant. 26 differential metabolites were found between P4 and P1, mainly organic acids and saccharides, of which, the most abundant ones are maltose, chenodeoxycholic acid, succinic acid, trehalose, fructose and threonine. There were 23 differential metabolites between P4 and P3, mainly organic acids, with succinic acid, chenodeoxycholic acid and threonine being the most abundant. P4 rhizosphere metabolites had the strongest chemotactic and growth-promoting effects on HZ13-RFP. 40 days after transplanting of tobacco seedlings, the count of HZ13 in P4 rhizosphere was 12.15 times higher than that in P3, accounting for 12.12% of the total rhizosphere bacteria, while P1 was 0. Compared with P3, P1 and CK, the maximum leaf area of seedlings was increased by 30%, 140% and 160% in P4, and plant height by 100%, 230% and 300%, respectively. In conclusion, the co-fermentation of cake fertilizer and Bacillus showed the best effects on the rhizosphere colonization of Bacillus and growth promotion of tobacco seedlings by Bacillus.