Methane (CH₄) and nitrous oxide (N₂O) emissions from rice fields are considered to be important sources of greenhouse gases. In order to clarify the emission characteristics of CH₄ and N₂O at different growth stages and to find optimal early season rice varieties and cultivation methods to control greenhouse gas emissions in southeast China, we conducted research in Jinhua City, Zhejiang Province, China in 2017 and 2018. Four different early season rice varieties were planted using three different rice establishment methods (machine transplanting, artificial transplanting, and direct seeding). The grain yield, CH₄, and N₂O emission rates and flux and economic profit were compared between the early varieties and establishment methods. Our results show that during the rice growth period, the CH₄ and N₂O emission fluxes and emission rates of the early season rice varieties increased first and then decreased, reaching the maximum at booting and the minimum at the grain filling stage. Direct seeding had the lowest cost and emission fluxes and emission rates compared to machine transplanting and artificial transplanting. The emission rates and flux of ‘Zhuliangyou609’ and ‘Zhongjiazao17’ were lower than in the other varieties. However, the yield of ‘Zhuliangyou609’ was higher than that of ‘Zhongjiazao17’ under identical conditions. Hence, direct-seeded rice shows good potential for cultivation in Zhejiang Province, and ‘Zhuliangyou609’ is the optimal early variety. This study provides theoretical support for the development of environmentally friendly early season rice establishment methods in southeast China.