Swelling is a common phenomenon in the vacuum packaging of lotus root during shelf life. This study determined the primary microbial species responsible for the swelling of vacuum-packaged lotus root firstly, then, the effect of 2,3-butanedione (0.125 and 0.250 g L−1) on the swelling and quality changes of lotus root were observed. The results showed that aerogens, such as Acetobacter, Enterobacter, and Aeromonas, were the primary microorganisms responsible for vacuuming lotus root bag swelling. 0.250 g L−1 of 2,3-butanedione showed the greatest inhibitory effect on lotus root bag swelling. Furthermore, the application of 2,3-butanedione treatment could delay the appearance quality and nutritional value deterioration of the lotus root, as well as avoid rancidity and preserve the smell of the root. These findings suggest that 2,3-butanedione treatment has potential practical applications in controlling bag swelling and preserving lotus roots in vacuum packaging.