Asparagus by-products are the promising resource that urgently need to be re-valorized. This study investigated the dynamic changes in physicochemical properties, organic acids, free amino acids, volatile flavor compounds, microbial succession, and their correlations during 7-day spontaneous fermentation of asparagus by-products. Dominant organic acids (lactic acid and acetic acid) and free amino acids (Ser, Glu, and Ala) increased with fermentation time, with lactic acid reaching 7.73 ± 0.05 mg/mL and Ser increasing 56-fold after 7 days. A total of 58 volatile flavor compounds were identified using headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPEM/GC-MS), with esters, alcohols and acids as the main volatile flavor compounds. Fourteen volatile flavor compounds had odor activity value >1. High-throughput sequencing showed Firmicutes and Proteobacteria as the main bacterial phyla, dominated by lactic acid bacteria (Levilactobacillus, Lactiplantibacillus, Weissella). Correlation analysis revealed that five bacterial genera (Levilactobacillus, Lactiplantibacillus, Enterobacter, Pediococcus and Acetobacter) were highly correlated with organic acids, free amino acids, and volatile flavor compounds, indicating their pivotal role in forming the characteristic flavor of fermented asparagus by-products (FAPS). This study provides new insights into the flavor and microbial profile of FAPS, offering a strategy for value-added processing and industrial production.