Durian fruit puree (DFP) is a nutrient-dense food, but it has a short shelf life. Presently, little research has been undertaken on extending the shelf life of DFP. Hence, it is necessary to develop treatment methods that can prolong the shelf life of DFP. In the present study, thermal processing (TP), high-pressure processing (HPP), and CO-assisted HPP (CO + HPP) treatments are used for DFP, and their influences on quality properties of DFP during storage (35 days, 4 °C) are investigated. Compared to other treatments, the CO + HPP treatment had a lower pressure and a shorter time to achieve the same effect of inactivating the microorganisms of DFP. During storage, CO + HPP treated DFP showed higher retention rates of sugars, total soluble solids, color, bioactive components, and antioxidant capacity in comparison with other treated DFPs. Moreover, after 35 days of storage, the microbial count of (CO + HPP)-treated DFP (3.80 × 10 CFU/g) was much lower than those of TP (4.77 × 10 CFU/g) and HPP (8.53 × 10 CFU/g)-treated DFPs. The results of this study reveal that CO + HPP treatment could not only better preserve the quality of DFP, but also effectively extend the shelf life of DFP, providing an effective method for the processing of DFP.