ANIR (Atacama Near InfraRed camera) is a near infrared camera for the University of Tokyo Atacama 1.0m telescope installed at the summit of Co. Chajnantor (5640m altitude) in northern Chile. The high altitude and the extremely low water vapor (precipitable water vapor:PWV=0.5mm) of the site enables us to perform observation of hydrogen Paschen alpha (Paα) emission line at 1.8751 μm. Since the first light observation in June 2009, we have succesfully obtained Paα narrow-band images of Galactic objects and near-by Galaxies. However, as there are many atmospheric absorption features within the wavelength range of the narrow-band filters which vary temporally due to change of PWV, it is difficult to calibrate the emission line flux accurately. Therefore, we have developed a new method to restore Paα emission-line flux from ground-based narrow-band filter imaging observations. First, average atmospheric transmittance within the narrow-band filter is derived using 2MASS stars in a image. Second, PWV is then estimated by comparing the transmittance with that calculated by atmospheric transmittance model software, ATRAN. Finally, the atmospheric transmittance at the wavelength of Paα emission-line is obtained from the model atmosphere corresponding to the obtained PWV. By applying this method to the data of nearby Luminous Infrared Galaxies obtained by ANIR, the emission line strength is estimated within the accuracy of 10% relative to that observed by HST/NICMOS. In this paper, we describe details of the calibration method and its accuracy.