Nowadays, our human life becomes machinery and increases mental stress. Yoga Meditation relieves our mental stress and re-establishes mental harmony when practiced regularly, and hence, it promotes physical, mental, and spiritual health. The previous studies on meditation show that there is relationship between mindful meditation, brain, and heart. As the meditation has direct impact on the mind power, the mental health is influenced by the depth of meditation. Also, brain and mind has the direct control over the heart, and physical health is indirectly related by mindful meditation. Experimental investigations on the effect of meditation are proposed by monitoring electroelectroencephalogram (EEG) with using brain-computer interface (BCI). The brain waves of the person who is under meditation will be captured using Neurosky BCI mind wave kit. The mental health status is analyzed by monitoring alpha, beta, and theta brain waves during long meditation. The impact of mediation on the heart rate variation (HRV), respiration rate, and blood pressure, etc., is monitored to evaluate the effectiveness of meditation on the physical health status. The captured brain waves through Neurosky BCI mindwave kit are filtered to get alpha and beta waves. The alpha and beta brain waves are analyzed using BCI Graphical User Interface (GUI) software tool to investigate the power levels of each wave and duration before and after meditation. The observed data was further analyzed through IBM Statistical Package for the Social Sciences (SPSS) tool for studying about mean, standard deviation, and variance of brain wave parameters, which shows the positive impact on physical as well as mental health parameters, especially cardiovascular (CV), and heart rate variation (HRV) parameters, etc.