Abstract: The present invention provides a method of reducing and controlling a hazardous substance in a process of high-value biological conversion of an urban organic waste. The method includes: 1) mixing a sludge, a first urban organic waste and an organic acid with water for acclimation to obtain an acclimatized sludge; 2) stage 1 of biological conversion: mixing the acclimatized sludge with a second urban organic waste to perform anaerobic culture; 3) stage 2 of biological conversion: adding nitrate and bacteria to continue anaerobic culture so as to obtain an organic acid. In the present invention, sludge microbes are acclimatized and then added to high-value chemicals such as acetic acid, propanoic acid and lactic acid prepared in biological conversion of the urban organic waste and then added with bacteria. Thus, by controlling pH value, microbe addition amount and nitrate concentration, the unfavorable effect of the antibiotics and heavy metal ions.