To comprehensively evaluate the quality of medicinal and edible Ziziphi Spinosae Semen (ZSS, the dried ripe seeds of Ziziphus jujuba var. spinosa) before and after rancidity during storage, some indicators including traditional sensory properties, physicochemical characteristics, and volatile compounds were analyzed. As a result, compared with the normal samples, the rancid samples of ZSS produced a darker color, a bitter taste, and an irritating odor, increased moisture content, electrical conductivity, fatty oil content, and acid value, and decreased water- and alcohol-soluble extract contents and pH value. Among them, the acid value had significant difference (p < 0.01) from 3.90 of normal ZSS to 18.68 mg/g of rancid ZSS. A total of 39 volatile compounds were identified in samples, including 20 in normal ZSS and 38 compounds in rancid ZSS. Nineteen common compounds were identified in normal and rancid samples. Among them, the content of 10 compounds such as δ-limonene, (R,R)-2,3-butanediol, and (R,S)-2,3-butanediol was decreased but that of nine compounds such as acetic acid, n-octanoic acid, and n-nonanoic acid was increased in rancid ZSS. Nineteen unique compounds such as β-phellandrene, α-pinene, and 3-carene were detected and only one compound, δ-cadinene, was not detected in rancid ZSS. In addition, eight short-chain organic acids, acetic, propanoic, butanoic, pentanoic, hexanoic, heptanoic, octanoic, and nonanoic acids, were new products in rancid ZSS, and it was speculated that the production of a series of organic acids might be the material basis of irritating odor after normal ZSS became rancid. This is the first report that a series of short-chain organic acids have been found in a rancid substance. In conclusion, there was a significant difference between normal and rancid ZSS. These indicators could be used as an early warning for judging the rancidity phenomenon of medicinal and edible ZSS. In addition, this is the first comprehensive evaluation about the rancidity process of a medicinal and edible substance.