The development of technology to improve the mineralization of organic fertilizer and to enhance crop production is essential to achieve the transition from traditional farming to eco-friendly organic farming. Nanobubble oxygation (NB) was employed for comparison with traditional pump-aerated oxygation (AW) and a control group through both soil incubation and soil column experiments. Plant-available N and P contents in the NB treatment group were higher than those in the AW and control groups. Enzymatic activities including β-1,4-N-acetyl-glucosaminidase, phosphatase, α-1,4-glucosidase, β-1,4-xylosidase, peroxidase, and phenol oxidase were significantly higher in both oxygation groups compared with the control. The soil microbial biomass, activity, and diversity were also significantly improved due to the oxygation treatment. Additionally, the microbial metabolic functions were shifted in both oxygation treatments compared with the control group. The final tomato yield increase from the NB treatment group was 23%, and that from the AW treatment was 17%, compared with the control.