To investigate the effect of greenhouse gas emission mitigation practices on a double-rice paddy field on the contents of amino acids in rice grains, sixteen amino acid derivatives under ten different treatments were analyzed. High-performance liquid-chromatography with an Agilent Zorbax AAA column was used, and an online pre-column derivatization method was adopted by using o-phthaldialdehyde (OPA) and 9-Fluorenylmethyl chloroformate (FMOC-CL) as the derivatization regent. Results showed that the rice grains of the ten treatments all included sixteen amino acids and species. When a combination of nitrogen fertilizer with addition of biochar at 48 t/hm² and intermittent irrigation (NPK+HBC+IF) was used as a treatment, the total amino acid contents were 6520.7 mg/100g, which was the highest in all treatments. Application of intermittent irrigation with no fertilizer was used as a control and this achieved the lowest total amino acid contents at 4338.0 mg/100g. The fraction of essential amino acids was highest at 36.8% in the control treatment. The nitrogen fertilizer with continuous irrigation (NPK+CF) treatment method achieved the lowest fraction of essential amino acids, at 33.1%. The contents of Aspartic Acid, Glutamic acid and Arginine in sixteen amino acids of rice grains were higher, while Methionine was lower in ten treatments. Second, with a treatment of nitrogen fertilizer with continuous irrigation, the total amino acid contents increased by 185.1 mg/100g and the fraction of non-essential amino acids increased by 3% in rice grains compared with a nitrogen fertilizer (the same amount) and intermittent irrigation treatment. The contents of Glutamic acid, Histidine and Serine were increased, while the content of Leucine was significantly decreased with the latter treatment. Third, the application of nitrogen fertilizer had a remarkable effect on the content of Histidine, and enhanced the amino acid contents in rice grains, which was increased with the increasing of nitrogen fertilizer application rates. Fourth, with the same amount of nitrogen fertilizer, the addition of pig manure resulted in an increase of 286.0 mg/100g in total amino acid contents, which indicated that addition of pig manure was better for the improvement of total amino acids contents in the condition of constant nitrogen fertilizer. Fifth, the rice straw incorporation treatment also increased the content of total amino acids and essential amino acids. The contents of Aspartic Acid, Glutamic acid and Histidine were increased, while the content of Methionine was decreased. The increase of returning crop straw obviously affected non-essential amino acid contents and the total amino acid contents were higher at half crop straw return (3 t/hm²). The total amino acid contents of total crop straw return with continuous irrigation (NPK+HRS+CF) was similar to that of the half crop straw return with intermittent irrigation treatment (NPK+LRS+IF), but the essential amino acid content was higher for the former. This phenomenon indicated that rice straw incorporation along with the management of water and nitrogen fertilizer might have an interaction effect on the content of amino acids. Finally, addition of biochar combined with nitrogen fertilizer greatly improved the essential and non-essential amino acid contents in rice grains, and its performance was positively correlated with its application rates. Based on these collective data, the addition of biochar in paddy fields performed better than other treatments for improving the total amino acid contents in rice grains, and this practice was beneficial for realistic production in rice fields and environment protection.