[Objective] Soil denitrification potential (SDP) is generally higher in paddy field than in upland field. However, as the effect of fertilization on SDP in paddy field and upland field varies with climatic and soil type, accuracy of its assessment is often affected by external conditions.[Method] In this study, two adjacent fields, one paddy field and one upland field, both derived from the same parent material of Quaternary red clay, in a long-term field experiment were selected for exploration of effect of fertilization regime on SDP and its association with abundances of functional genes (narG, nirS, nirK, and nosZ) and community composition of nirS-type denitrifiers with the aid of in-lab incubation, real-time quantitative polymerase chain reaction (qPCR), and high-throughput sequencing technology.[Result] In the paddy field, compared with Treatment NPK, Treatment NP and PK was significantly or 33.01% and 23.57%, respectively, higher in SDP, while Treatment NK was 35.76% lower in SDP. The effects of Treatments NP and NK were related to the abundance of nirS gene, and the changes in content of soil available P (AP) and N:P ratio, while that of Treatment PK was associated with the community composition of nirS-type denitrifiers (Azospira sp. NC3H-14). In the upland field, compared with Treatment NPK, Treatment NP, NK and P was 13.94%, 26.51%, and 25.41%, respectively, higher in SDP. The effects of Treatments NK and P were significantly related to the abundance of narG gene and of nirS-type denitrifiers (Azospira sp. NC3H-14 and Ideonella sp. NC3L-43b for NK treatment; Azospira sp. NC3H-14, Rhodanobacter sp. D206a, Rubrivivax gelatinosus for P treatment). The content of amorphous iron oxide (Feo) was probably the main factor affecting the abundance of narG gene.[Conclusion] The above listed findings indicate that planting system affects the effect of fertilization on SDP. The variation of SDP in paddy field is mainly attributed to nirS-type denitrifiers, while that in upland field primarily to the abundance of functional gene and the community compostion of nirS-type denitrifiers.