To compare the effects of different fertilization methods on the fruit quality of ‘Zao Hong’ navel in Zigui County, Yichang City, Hubei Province, a field experiment was conducted in the ‘Zao Hong’ navel orchard in Guiya Village, Jiuwanxi Town, Zigui County. The experiment had 4 treatments: applying the Aija microbial formula fertilizer (treatment 1), applying Kangpu microbial formula fertilizer (treatment 2), conventional fertilization (treatment 3), and no fertilization (control group). Each treatment had 20 replicates. The research results showed that compared with no fertilization, the fruit weight per single fruit, fruit flesh weight, transverse diameter, longitudinal diameter, and fruit shape index of the conventional fertilization treatment were significantly increased by 69.23%, 77.92%, 56.61%, 21.69%, and 26.39%, respectively. The content of titratable acid was significantly reduced by 12.36%, and the total sugar content was significantly increased by 14.52%. The ratios of solid acid and sugar acid were significantly increased by 15.44% and 30.00%, respectively. The content of Vc was significantly increased by 11.40%. Applying the Aijia microbial formula fertilizer significantly increased the fruit weight per single fruit, fruit flesh weight, transverse diameter, and longitudinal diameter by 80.46%, 99.77%, 43.72%, and 19.78%, respectively. The hardness of the fruit skin was significantly reduced by 7.13%, and the content of titratable acid was significantly decreased by 23.60%, and the total sugar content was significantly increased by 27.42%. The ratios of solid acid and sugar acid were significantly increased by 51.08% and 65.71%, respectively. The protein and Vc contents were significantly increased by 87.77% and 17.51%, respectively. Applying the Kangpu microbial formula fertilizer significantly increased the fruit weight per single fruit, fruit flesh weight, transverse diameter, and longitudinal diameter by 95.07%, 117.87%, 53.05%, and 26.48%, respectively. The content of titratable acid was significantly decreased by 28.09%, and the total sugar content was significantly increased by 32.26%. The ratios of solid acid and sugar acid were significantly increased by 55.33% and 82.86%, respectively. The protein and Vc contents were significantly increased by 56.12% and 23.14%, respectively. Thus, both applying microbial formula fertilizers and conventional fertilizers have significant effects on improving the fruit quality of ‘Zao Hong’ navel in Zigui. The effect of applying the Kangpu microbial formula fertilizer is the most significant, followed by applying the Aijia microbial formula fertilizer.