The production of short-chain fatty acids (SCFAs) through anaerobic fermentation of waste activated sludge (WAS) is commonly constrained by limited substrate availability, particularly for WAS with low organic content. Combining the hydrocyclone (HC) selection with alkali-thermal (AT) pretreatment is a promising solution to address this limitation. The results indicated that HC selection modified the sludge properties by enhancing the ratio of mixed liquid volatile suspended solids (MLVSS)/mixed liquid suspended solids (MLSS) by 19.0% and decreasing the mean particle size by 17.4%, which were beneficial for the subsequent anaerobic fermentation process. Under the optimal HC + AT condition, the peak value of SCFAs production reached 4951.9 mg COD/L, representing a 23.2% increase compared to the raw sludge with only AT pretreatment. Mechanism investigations revealed such enhancement beyond mechanical separation. It involved an increase in bound extracellular polymeric substances (EPS) through HC selection and the disruption of sludge spatial structure by AT pretreatment. Consequently, this combination pretreatment accelerated the transfer of particulate organics (i.e., bound EPS and intracellular components) to the supernatant, thus increasing the accessibility of WAS substrate to hydrolytic and acidifying bacteria. Furthermore, the microbial structure was altered with the enrichment of key functional microorganisms, probably due to the facilitation of substrate biotransformation and product output. Meanwhile, the activity of hydrolases and SCFAs-forming enzymes increased, while that of methanogenic enzymes decreased. Overall, this strategy successfully enhanced SCFAs production from WAS while reducing the environmental risks of WAS disposal.