The method of nutrient flow was adopted to compare farmers’ nutrient management behaviors in 2007 between biogas and non-biogas farmer’s household in 13 investigated sites which included Sichuan, Guangxi, Heibei, et al. provinces. The results showed the total amount of nutrient for putting was only 781.62 kg/hm2 in biogas household, which was significantly lower than 850.82 kg/hm2 that put into no-biogas farmers' household. The two groups’ farmers had no significant difference in fertilizer and straw nutrient for putting to field per hectare; the amount of straws used as fuel for household was significantly decreasing，while the percentage which was burned in field was increasing in some investigated regions. But the percentage of manure putting into field in no-biogas farmers’ household was 96%, and that was only 39% in biogas farmers’ household. A great deal of manures put into biogas plants was not recycled into crop field. The percent of nutrient in biogas residue was only 9% of the total amount of nutrient returning to field. From a nutrient recycling view, the nutrient cycling efficiency of biogas farmers was 45%, which was only 64% of that in no-biogas farmers. Therefore, the booming development of biogas system in farmers household did not reduce the consumption of chemical fertilizer, and did not improve the recycling of organic nutrient. Although biogas system in farmers household eliminate nutrient loss from manure in somewhere, the farmers should be trained to use their crop residue properly, to understand the function of biogas residue as fertilizer and to use it reasonably. By this way, biogas system can be really used to improve nutrient problem in China.