The discovery of Comammox（complete ammonia oxidizers）is considered to be an important progress in the study on nitrogen recycling, but further efforts need to be done to elucidate environmental driving mechanisms of the coexistence of Comammox with AOA（ammonia-oxidizing archaea）and AOB（ammonia-oxidizing bacteria）in the complex soil environment. Soil samples were collected from a long-term stationary experiment on purple paddy soils, which had two treatments, i.e. PF (plant rice in summer and keep the field flooded all the year) and FD (fallow all the year and keep the field dried up in winter), for analysis of effects of fertilization and water management on nitrification potential and abundance of ammonia-oxidizing microorganisms in paddy soils. The analysis shows that PF was higher than FD in nitrification potential, which reached 25.0 mg•kg^-1•d ^-1 and 2.11 mg•kg^-1•d ^-1, respectively. Obviously, the former was 12 times as high as the latter. Real-time quantitative PCR (Q-PCR) shows that Comammox, AOA and AOB were detected in the paddy soils of PF and FD, and displayed an order of Comammox> AOA>AOB in abundance. The abundance of Comammox was 8.5 times that of AOA and 77.3 times that of AOB in the PF paddy soil, and 4.1 times that of AOA and 490.3 times that of AOB in the FD paddy soil. Compared with FD, PF stimulated growth of the Comammox Clade A, AOA and AOB in the soil, making the three 9, 3 and 42 times higher, respectively, in population. But the Comammox Clade B dropped 2 times as fast. All the findings in the 28 year-long experiment indicate that compared with FD, PF keeps ammonia-oxidizing microorganisms in the paddy soils under the long-term stress of O2 deficiency and selectively promotes growth of the Comammox Clade A and AOA in the soils, while fertilization at a high rate significantly promotes growth of the AOB; and Comammox Clade A and AOA can adapt to a wide range of ammonium nitrogen substrates. In future, the technique of DNA-SIP (stable isotope probe) may be used to identify functional significance of Comammox, which is dominant in population in paddy soils and its relative importance to AOA and AOB.