Industry-scale microfluidizer system (ISMS) is a novel equipment for producing filtered-free whole beverages. This study investigated the color, nutrition, and flavor changes of whole mango juice (WMJ) treated by ISMS under various pressure (0–120 MPa). Results showed that ISMS well maintained the total soluble solid content, pH value, and yellow color of WMJ. The carotenoids were not destroyed with treatment pressure below 90 MPa, and the carotenoids bioaccessibility of all the WMJ samples was no change. More importantly, ISMS promoted the release of ascorbic acid and total polyphenols by disrupting cellular integrity, thus improving antioxidant activities of WMJ. Volatile compounds analysis found that WMJ samples had more terpenes and aldehydes when treated at 90 MPa, and possessed more esters at 120 MPa. These results demonstrated that ISMS might offer new opportunities to produce WMJ with excellent qualities at an industrial level.