Bioactive organic compounds (BOCs) contained in bio-stabilized products of waste activated sludge (WAS) have attracted considerable attention, as they can enhance the fertilizing effect of WAS in land applications. This study investigated the molecular composition and plant-growth-promoting mechanisms of various BOCs in the bio-stabilized products of WAS. After stepwise fractionation, aerobic composting sludge (ACS) and anaerobic digestion sludge (ADS) were chemically fractioned into five subcomponents, namely dissolved organic matter (DOM) (C1), weakly interacted organic matter (OM) (C2), metal-bonded OM (C3), NaOH-extracted OM (C4), and strongly interacted OM (C5), in sequence. The results showed that fatty acids and carboxylic acid (CAs) present in ACS C2 promoted plant growth and enhanced the ability of plants against stresses by upregulating pathways related to “carbohydrate metabolism,” “lipid metabolism,” “amino acid metabolism,” and “phenylpropanoid biosynthesis.” However, in ACS C4, plenty of amino acids could promote plant growth via upregulating “carbohydrate metabolism” and “amino acid metabolism” pathways. As an important precursor, aromatic amino acids inside ACS C4 also stimulated the production of indoleacetic acids. In ADS C1, amino sugar and phytohormone were the major BOCs causing the up-regulation of “carbohydrate metabolism” and AAA catabolism in “amino acid metabolism” pathways. CAs enriched in ADS C2 stimulated plant growth through “amino acid metabolism” pathway. In summary, alkali extraction can recycle a large proportion of BOCs with low environmental risk from the bio-stabilization products of WAS. The results from this study provide scientific guidance for safe and value-added resource utilization of bio-stabilization products of WAS in land applications.