There is limited information about the influences of long-term fertilizer management on methane (CH4) and nitrous oxide (N-2O) emissions from double-cropping paddy fields in Southern China. Therefore, the objective of the present study was to characterize the changes of CH4 and N2O related to different fertilizer treatments based on a long-term field experiment. The experiment was initiated in 1986 and consisted of five treatments: unfertilized (CK), mineral fertilizer alone (MF), rice residues plus mineral fertilizer (RF), low manure rate plus mineral fertilizer (M1 + F), and high manure rate plus mineral fertilizer (M2 + F). Investigations were conducted over 2 years, from 2013 to 2014, to examine the CH4 and N(2)Oemissions from paddy field of Southern China. The results indicated that M2 + F plots had the largest CH4 emissions during the early rice and late cropped rice and that MF and RF had larger N2O emissions than CK in both early and late cropped rice. When compared with the control, total N2O emissions in both rice-growing seasons increased in both MF and RF in 2013 and 2014. The global warming potentials (GWP) from paddy fields were ranked as M2 + F > M1 + F > RF > MF > CK. Meanwhile, the results demonstrated that CH4 and N2O emissions were closely associated with the soil redox potential and soil temperature. In summary, the incorporation of rice residues in addition to the use of mineral fertilizer (RF treatment) may be an effective fertilizer management practice for mitigating total GWP per grain yield and maintaining rice grain yield in southern China.