This study was conducted to establish a hazard analysis and critical control point (HACCP) system for preserving pleasant flavor in raw milk and study its feasibility for application. One thousand lactating cows raised in a dairy farm in the suburb of Huhhot were used as experimental animals. The experiment lasted for 90 d, which consisted of a control period (1 to 30 d, ordinary feeding and management regime) and an experimental period (31 to 90 d, HACCP system). Raw milk samples were collected for the analysis of physical and biochemical indices, concentration of volatile flavor compounds, sensory and flavor intensity index (FII), as well as sensory score. The results showed as follows: 1) after performing the HACCP system, no significant changes were found in percentages of milk fat, milk protein, milk lactose and dry matter, as well as acidity and antibiotics index (P>0.05), but acidity was slightly reduced, and antibiotic index tended to be improved; total number of bacteria significantly decreased (P<0.05); milk yield was significantly increased (P<0.05). 2) There were differences in type and concentration of volatile flavor compounds before and after performing the HACCP system, which induced the difference of milk flavor, and sensory evaluation scores increased slightly after performing the HACCP system (P>0.05). 3) FII of raw milk from different origins was increased after performing the HACCP system; milking and storage process affected milk flavor at the most. The HACCP system for preserving pleasant flavor in raw milk is established in the present study, and it can not only preserve milk pleasant flavor, but also improve milk quality.