An algorithm is proposed to calculate the whole atmospheric aerosol optical depth (AOD) with aerosol scale height based on micro-pulse lidar data. Vertical extinction coefficient profiles and surface horizontal extinction coefficient of aerosol can be retrieved with the data vertically and horizontally measured by lidar. The vertical extinction coefficient profiles of aerosol are classified into four types, and different fitting methods are utilized to obtain aerosol scale height. Aerosol scale height is combined with surface extinction coefficient to calculate the whole atmospheric AOD. Comparison is made between the calculated results and those measured by sun-photometer in the same area simultaneously, and we find that the compared results show a good agreement. The average relative error is less than 6.7%. The proposed method provides a new technological means to calculate atmospheric AOD during the partly cloudy conditions and the night.