This study aims to investigate the effect of brain-based small muscle coordination exercise program on the cognitive function, brainwave intrinsic rhythm, and brain regions of the elderly. For this purpose, analysis was performed for the results of tests conducted on 18 seniors in the experimental group and 17 seniors in the control group aged 65 years or older who used senior welfare centers located in ㅇ-gu, ㅇ-si of Korea. In order to test the effectiveness of the brain-based small muscle coordination exercise program during this research, the MMSE-DS questionnaire was used for the subjects and the 8-channel electroencephalogram test was performed. As a result of the test, the mean value of the MMSE-DS after running the program was significantly higher in the experimental group and significantly lower in the control group compared to the average value before running the program. For the brain wave intrinsic rhythm (PF), the experimental group after running the program showed a significant increase in the Fp1 and Fp2 regions compared to that before running the program. For the inter-correlation mapping for each brain region, the experimental group showed higher inter-correlation between F3-F4, F4-T3, F3-T4, T3-P4, T4-P3, and P3-P4, and the control group showed lower inter-correlation, when comparing before and after the program. Looking at the above results, it is considered that the brain-based small muscle coordination exercise program can help suppress physiological aging and prevent and delay dementia by encouraging left and right brain coordination and stimulating the sensory areas of the peripheral nerves.