Objective: The aim of this study is to classify between intentional and natural blinks in vision based eye tracking system. Through implementing the classification method, we expect that the great eye tracking method will be designed which will perform well both navigation and selection interactions. Background: Currently, eye tracking is widely used in order to increase immersion and interest of user by supporting natural user interface. Even though conventional eye tracking system is well focused on navigation interaction by tracking pupil movement, there is no breakthrough selection interaction method. Method: To determine classification threshold between intentional and natural blinks, we performed experiment by capturing eye images including intentional and natural blinks from 12 subjects. By analyzing successive eye images, two features such as eye closed duration and pupil size variation after eye open were collected. Then, the classification threshold was determined by performing SVM(Support Vector Machine) training. Results: Experimental results showed that the average detection accuracy of intentional blinks was 97.4% in wearable eye tracking system environments. Also, the detecting accuracy in non-wearable camera environment was 92.9% on the basis of the above used SVM classifier. Conclusion: By combining two features using SVM, we could implement the accurate selection interaction method in vision based eye tracking system. Application: The results of this research might help to improve efficiency and usability of vision based eye tracking method by supporting reliable selection interaction scheme.