In this study, samples of two acidic soils (JX-3 and JX-7) with similar initial pH were selected for incubation experiments to study the roles of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the nitrification of acidic soils. The results showed that after 50 d incubation, the nitrification rate of JX-7 sample was significantly higher than that of JX-3, and soil pH was significantly reduced. After incubation, AOB abundances of two soil samples increased, but there was no significant difference between two soil samples; AOA abundance of JX-7 significantly increased, while JX-3 changed insignificantly. AOA community structures of two soil samples were different, but there was no significant difference between incubation time; AOB community structures of two soil samples had the similar community structure, but they were different between incubation time. After incubation, the absolute abundances of dominant AOA (e.g., Nitrososphaera and some unknown microbes) in JX-7 sample significantly increased; the absolute abundances of some AOB such as Nitrosospira in both two samples significantly increased. Therefore, AOA played an important role in nitrification of acidic soil studied; and AOA mainly regulated nitrification by increasing the abundances of individual OTUs such as Nitrososphaera rather than the entire community.