Cloud loss of orange juice could be effectively inhibited by centrifugal treatment, but it can induce flavor changes, which become a new challenge for the industry. This work aims to investigate the effect of centrifugation on flavor changes in orange juice and explore its possible mechanism. Taste- and aroma-related attributes were analyzed, and pectin was characterized. Results indicated that pH (4.00), total soluble solid (9.67 °Brix), titratable acidity (0.42%), sucrose (44%), fructose (29%), and glucose (27%) were less affected by centrifugation (P > 0.05). However, aroma compounds significantly changed (P < 0.05), where terpenes and alcohols tended to be distributed in pulp and serum after centrifugation, respectively. Pearson correlation analysis showed that aroma compound distribution induced by centrifugation was highly related to chelator-solubilized pectin fraction and sodium carbonate-solubilized pectin fraction (|R| > 0.9). In general, centrifugation clearly changed aroma of orange juice, which was mainly affected by pectin characteristics.