Postharvest Physiological Deterioration (PPD) presents a substantial challenge to the global cassava industry, underscoring the critical need to extend shelf life. This study investigated the impact of hypobaric storage on postharvest quality during storage. A notable effect was observed, with the inhibition of cassava PPD evident under 0.06 MPa, in a decrease of 2.47% in water content and 2.28% in weight loss after 20 days of storage in cassava tuberous roots. The results from water migration and magnetic resonance imaging affirmed the crucial role of maintaining stable moisture content during storage. Furthermore, the treatment group obviously inhibited CAT activity and SOD activity had no significant (p < 0.05) during storage, surpassing those observed in the control group. Notably, the expression of both phenylalanine metabolism gene and enzyme activity was lower under 0.06 MPa. In conclusion, based on the outcomes of this study, we recommend a storage pressure of 0.06 MPa for cassava roots to mitigate the occurrence of PPD and enhance overall storage quality.