The effect of packaging material and storage temperature on two types of soy sauce was investigated. Ethanol content decreased significantly in all tested samples after storage ( < 0.05). While the changes of physicochemical properties and CIELAB color space indexes varied with soy sauce types, packaging materials and storage temperatures. The changes of volatile profiles after storage indicated that storage temperature was a key factor resulting in flavor scalping. It also suggested that there was no significant difference of flavor compounds sorption between glass bottle and polyethylene terephthalate bottle. The abundances of acids and alcohols increased after stored at ambient temperature (AT) and low temperature (LT) for 90 days, but phenols decreased. The effect of the packaging material, raw soy sauce type and storage temperature resulted in changing the intensities of fruity, caramel-like, mushroom-like note as well as smoky note. For the inoculated soy sauces, 1-octen-3-ol, ethyl hexanoate and ethyl octanoate in the samples were dominant in samples stored at AT, while the samples stored at LT were characterized by multiple components according to the results of principal components analysis. These results were benefit for understanding the main factors affecting the flavor profiles and quality of soy sauce during storage, as well as optimizing the storage condition.