The invention discloses a green micro-ecological compound fertilizer and a preparation method thereof. The green micro-ecological compound fertilizer is prepared from the following raw materials in parts by weight: 30-60 parts of a bio-organic fertilizer base material, 8-20 parts of liquid biological bacteria, 5-18 parts of modified starch and 18-25 parts of aerated concrete powder. The micro-ecological compound fertilizer has the characteristics of greenness, environment-friendliness and high efficiency. Besides, the aerated concrete powder and the modified starch are added into the compound fertilizer. A large number of micro-pores are formed in the surface and the interior of the aerated concrete powder, and the aerated concrete powder can serve as a filling carrier of organic fertilizer and biological bacteria. The modified starch, on one hand, plays a role in bonding, and on the other hand, the ionic groups in the modified starch are matched with the aerated concrete powder to form a spatial net-shaped structure, so that organic fertilizer and biological bacteria in the fertilizer particles are fully fixed and cannot directly collapse and lose when encountering water, and the micro-porous structure can always keep stable emission of the fertilizer, so that the environmental tolerance of the compound fertilizer is effectively improved, and the long-term stability of the fertilizer efficiency is ensured.