Yellow clay paddy soil (Oxisols) is a typical soil with low productivity in southern China. Nitrification inhibitors and slow release fertilizers have been used to improve nitrogen fertilizer utilization and reduce environmental impaction of the paddy soil. However, their effects on ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in paddy soil have rarely been investigated. In the present work, we compared the influences of several slow release fertilizers and nitrification inhibitors on the community structure and activities of the ammonia oxidizers in yellow clay soil. The abundances and community compositions of AOA and AOB were determined with qPCR, terminal restriction fragment length polymorphism (T-RFLP), and clone library approaches. Our results indicated that the potential nitrification rate (PNR) of the soil was significantly related to the abundances of both AOA and AOB. Nitrogen fertilizer application stimulated the growth of AOA and AOB, and the combinations of nitrapyrin with urea (NPU) and urea-formaldehyde (UF) inhibited the growth of AOA and AOB, respectively. Compared with other treatments, the applications of NPU and UF also led to significant shifts in the community compositions of AOA and AOB, respectively. NPU showed an inhibitory effect on AOA T-RF 166 bp that belonged to Nitrosotalea. UF had a negative effect on AOB T-RF 62 bp that was assigned to Nitrosospira. These results suggested that NPU inhibited PNR and increased nitrogen use efficiency (NUE) by inhibiting the growth of AOA and altering AOA community. UF showed no effect on NUE but decreased AOB abundance and shifted AOB community.