Proper rice straw management in paddy fields is necessary in order to sustain soil productivity and reduce greenhouse gas emissions. A field experiment was carried out from 2008 to 2011 in subtropical China: (1) to monitor rice yield, soil available nutrients, CH4, and N2O emissions and (2) to evaluate the effects of timing of rice straw incorporation and joint N application rate in a double rice cropping system. The total amount of rice straw from one cropping season was incorporated in winter (W-S) or in spring (S-S) and mineral N was jointly applied with rice straw incorporation at rates of 0, 30, and 60 % of the basal fertilization rate (N-0B, N-30B, and N-60B) for the first rice crop. Soil water was naturally drained during the period of winter fallow (P-WF) and controlled under intermittent irrigation during the period of first rice growth (P-FR). Compared with S-S, W-S significantly (P < 0.05) increased the first rice yield only in the flooding year (2010), and increased the soil available K concentration after P-WF and P-FR in 2008-2009 and the hydrolysable N concentration after P-WF in 2010-2011. Meanwhile, W-S significantly decreased the total CH4 emission by about 12 % in 2009-2010 and 2010-2011, but increased the total N2O emission by 15-43 % particularly during P-WF in all 3 years, resulting in a lower GWP in W-S in the flooding year and no differences in the nonflooding years. Compared with N-0B, joint N application (N-60B and N-30B) increased the soil hydrolysable N after P-WF in all 3 years. Meanwhile, it decreased the total CH4 emissions by 21 % and increased the N2O emissions during P-WF by 75-150 % in the nonflooding years, but the net GWP was lower in N-60B than in N-0B. The results suggested that the rice straw incorporation with joint N application in winter is more sustainable compared with the local practices such as rice straw incorporation in spring or open-field burning.