Abstract: Traditional Egyptian cheese has a long history and holds an important place in the local culinary culture. However, systematic studies on the flavor compounds, microbial community structure, and their interrelationships in traditional Egyptian cheese remain limited. To ensure quality stability, this study systematically analyzed the characteristic flavor components and microbial community compositions of Mish and Karish cheeses by determining their physicochemical properties, organic acid content, and free amino acid content using headspace solid-phase microextraction gas chromatography-mass spectrometry and high-throughput sequencing techniques. The results showed that both were soft cheeses with high protein and low fat. Eight organic acids were detected, with lactic acid (70.54%) being the predominant component. Sixteen free amino acids were identified, of which essential amino acids accounted for 60.51%. Volatile compound analysis identified 86 volatile components, with 29 recognized as key aroma compounds (odor activity value ≥ 1). Among these, 2-nonanol, phenethyl alcohol, ethyl octanoate, ethyl decanoate, and ethyl hexanoate were common aroma compounds across all samples and formed the core aroma profile of traditional Egyptian cheeses. High-throughput sequencing revealed that the bacterial communities mainly consisted of Lactobacillus and Streptococcus, while the fungal communities were dominated by Kodamaea, Dipodascaceae, Torulaspora, and Metschnikowia, of which Torulaspora exhibited higher abundance in Karish cheese. Spearman correlation analysis indicated that Weissella and Kodamaea were closely associated with the development of cheese flavor, showing positive correlations with various amino acids, organic acids, and volatile compounds, and negative correlations with 2-dodecanol, 2-heptanol, isoamyl acetate, and ethyl acetate. Additionally, Streptococcus, Lactococcus, Candida, and Kluyveromyces also contributed significantly to cheese flavor development by participating in the synthesis of tartaric acid and certain ethyl esters. These findings provide novel insights into the microbial-driven flavor formation mechanism and a theoretical basis for screening industrial starter cultures and flavor regulation in traditional Egyptian cheese.