By using the method of static chamber-gas chromatographic techniques, methane emission flux from late rice fields were studied under different long-term fertilizing systems. The results showed that, methane emission from late rice fields from different fertilizing systems differed with seasonal variation, and represented an increasing at the beginning and declining later on. Methane emission flux and accumulation emission flux of straw manure treatment was significantly higher than that of all other treatments; Methane emission flux and accumulation emission flux differed between different nutrients deficiencies. Methane emission flux and accumulation emission flux of straw manure treatment was higher than that of inorganic total nutrient treatment. Methane accumulation emission fluxes were the lowest under non- or partial- fertilizer treatments. The environmental factors of different long-term fertilizing systems affecting methane emission from late rice fields were discussed, including soil temperature, water depth and soil Eh. Under different long-term fertilizing systems, there was a significantly positive correlation between CH4 emission flux and soil temperature and a significantly negative correlation between CH4 flux and soil Eh. No significant correlation was found between CH4 flux and water depth.