The invention provides a micro-molecular biological controlled-release composite fertilizer which comprises the following components in parts by weight: 10-20% of urea, 15-30% of monoammonium phosphate, 10-25% of potassium sulfate and/or potassium chloride, 5-10% of micro molecular nitrogen powder, 15-20% of medium trace element powder, 15-20% of a slow-release organic matter mixed material and 0.2-0.6 per mill of a composite bacterium, wherein the content of nitrogen of micro molecular nitrogen powder is 30-40%; the medium trace elements comprise raw material powder of potassium, calcium, magnesium, sulfur, zinc, iron, boron, manganese and ore; the slow-release organic matter mixing material comprises byproducts of stevia rebaudiana powder, humic acid and soyabean protein; the effective bacterium content of the composite bacterium is 30-40 billion/gram. The invention further provides a preparation method of the micro-molecular biological controlled-release composite fertilizer. Therefore, the micro-molecular biological controlled-release composite fertilizer is not only relatively high in fertilizer efficiency, but also capable of ensuring that plants relatively well absorb metal elements.