Upland red soils have been identiifed as major CO2 and N2O sources induced by human activities such as fertilization. To monitor characteristics of soil surface CO2 and N2O lfuxes in cropland ecosystems after continuous fertilizer applications over decades and to separate the respective contributions of root and heterotrophic respiration to the total soil CO2 and N2O lfuxes, the measurements of soil surface CO2 and N2O lfuxes throughout the maize growing season in 2009 were carried out based on a fertilization experiment (from 1990) through of the maize (Zea mays L.) growing season in red soil in southern China. Five fertilization treatments were chosen from the experiment for study: zero-fertilizer application (CK), nitrogen-phosphorus-potassium (NPK) fertilizer application only, pig manure (M), NPK plus pig manure (NPKM) and NPK with straw (NPKS). Six chambers were installed in each plot. Three of them are in the inter-row soil (NR) and the others are in the soil within the row (R). Each fertilizer treatment received the same amount of N (300kg ha-1 yr-1). Results showed that cumulative soil CO2 lfuxes in NR or R were both following the order: NPKS>M, NPKM>NPK>CK. The contributions of root respiration to soil CO2 lfuxes was 40, 44, 50, 47 and 35%in CK, NPK, NPKM, M and NPKS treatments, respectively, with the mean value of 43%. Cumulative soil N2O lfuxes in NR or R were both following the order: NPKS, NPKM>M>NPK>CK, and soil N2O lfuxes in R were 18, 20 and 30%higher than that in NR in NPKM, M and NPKS treatments, respectively, but with no difference between NR and R in NPK treatment. Furthermore, combine with soil temperature at -5 cm depth and soil moisture (0-20cm) together could explain 55-70% and 42-59% of soil CO2 and N2O emissions with root interference and 62-78%and 44-63% of that without root interference, respectively. In addition, soil CO2 and N2O lfuxes per unit yield in NPKM (0.55 and 0.10kg Ct-1) and M(0.65 and 0.13g Nt-1) treatments were lower than those in other treatments. Therefore, manure application could be a preferred fertilization strategy in red soils in South China.