Cognitive assessment has a broad application prospect, including estimate of childhood neuro development and maturation, diagnosis of neurodegenerative diseases, and selection for special profession. With the development of computer technique and behavioral recording sensors, the method of cognitive assessment has been replaced from paper scale test to human–computer interaction. We can not only obtain the results of tasks, but also make it possible to acquire multiple behavioral and physiological data during the task. However, there is still a strong challenge of recording multi-source data synchronously during multi-dimensional cognitive assessments. Therefore, we built a multi-source cognitive assessment system can record multi-pattern behavioral and physiological data and feedback at different spatiotemporal levels. Under this system, we developed a multi-source diagnostic toolset for cognitive assessment, including eye tracking, hand movement, EEG and human–computer interaction data during the cognitive task. 238 participants with different mental disorders were assessed using this system. The results showed that our diagnostic toolset can be used to study the behavioral abnormalities of patients with mental disorders through the characteristics of multi-source data. Furthermore, this system can provide some objective diagnostic criteria such as behavioral characters and EEG features for diagnosis of mental disorders.