The invention provides a biological water soluble fertilizer and a preparation method thereof. The biological water soluble fertilizer is prepared from the following components in parts by weight: 8-15 parts of bacillus subtitles, 38-50 parts of humic acid amine, 5-10 parts of amino acid, 2-4 parts of acetic acid, 5-10 parts of Chinese herbal medicine components, 18-30 parts of inorganic fertilizer based on N+P2O5+K2O and 4-8 parts of medium trace elements. The invention also provides a method for preparing the biological water soluble fertilizer. The plant probiotics, the Chinese herbal medicine components, probiotic acids and the medium trace elements are organically combined, and according to the antagonism and growth promotion of microbes, immune activation of the Chinese herbal medicines and multiple organic acids and nutritional supplement effects of the medium trace elements, the biological water soluble fertilizer has the effect of guaranteeing the plant health in an all-around mode and is non-toxic and harmless.