In this study, we determined the alignment of the laser altimeter aboard Hayabusa2 with respect to the spacecraft using in-flight data. Since the laser altimeter data were used to estimate the trajectory of the Hayabusa2 spacecraft, the pointing direction of the altimeter needed to be accurately determined. The boresight direction of the receiving telescope was estimated by comparing elevations of the laser altimeter data and camera images, and was confirmed by identifying prominent terrains of other datasets. The estimated boresight direction obtained by the laser link experiment in the winter of 2015, during the Earth's gravity assist operation period, differed from the direction estimated in this study, which fell on another part of the candidate direction; this was not selected in a previous study. Assuming that the uncertainty of alignment determination of the laser altimeter boresight was 4.6 pixels in the camera image, the trajectory error of the spacecraft in the cross- and/or along-track directions was determined to be 0.4, 2.1, or 8.6 m for altitudes of 1, 5, or 20 km, respectively.