The invention discloses an active micromolecular ecological nutrition agent and a use method thereof. The nutrition agent is obtained by taking organic waste as the raw material, carrying out subcritical water treatment under 180-280DEG C and 1.2-7.5Mpa for 40-90min, and then performing solid-liquid separation. In a solid fertilizer, the content of organic matters is 70-90%, the content of total nutrients is 4-6%, the content of amino acid is greater than or equal to 20%, the content of humus is greater than or equal to 45%, the content of trace elements is greater than or equal to 0.5%, and the pH is 4-6. In a liquid fertilizer, the content of organic matters is 50-120g/L, the content of total nutrients is 500-950mg/L, the content of amino acid is greater than or equal to 10g/L, the content of humus is greater than or equal to 20g/L, the content of trace elements is greater than or equal to 200mg/kg, and the pH is 4-6. According to the use method, in addition to be used for topdressing, the solid fertilizer can be applied individually or mixed with other fertilizers, can be used for furrow fertilization, row fertilization, hole fertilization or spray fertilization and rotary tillage, and the dosage for every 666.67 square meters is 200-850kg. The liquid fertilizer can be used for flushing fertilization, jet fertilization, spray fertilization or drop irrigation with water, and the dosage for every 666.67 square meters is 20-200kg. The organic fertilizer involved in the invention has higher fertilizer efficiency and activity, can make fruit tree single fruit reach a weight gain of 7-15%, melons and fruits reach a yield increase of 10-20%, grains reach a yield increase of 5-16%, and vegetables reach a yield increase of 8-20%. Also, the quality, growth and soil indexes are improved, fertilizer consumption is greatly reduced, resources are saved and environmental protection is achieved.