As per the government statistics Indian higher education system is estimate to be the largest in the world, and is expected to increase to US$ 37.8 billion by 2020.Thus India can emerge as the strong intellectual hub of the world which direct ours study to focus towards the academic excellence of Higher education Institution .The drivers to this academic excellence witnessed in organization performance of the organizations are the employees of the organization. Hence our research focus on investigation the relation between the employee motivation and Organizational performance in higher education institutions. The paper has two major objectives to indentify the factors of motivation existing in higher education institution and 2) to investigate the relation between the employee motivation and organizational performance Higher education institutions in India. The study utilizes factor analysis to get the understanding of our objective. A self administered questionnaire was gathered form 204 respondents as faculties of higher education institution with diverse disciple. Research showed a significant relation between the various and provide an opportunities to management of the institution to understand the polices to effective governance so that organization academic excellent can be achieved.