The present invention provides a lens substrate stacking position calculating apparatus capable of calculating a stacking position at which the number of lens sets whose optical axis deviation falls within an allowable range is maximized, when a plurality of wafer lens arrays are bonded together even if the position of each lens formed on a wafer substrate is deviated between wafer lens arrays to be stacked. The lens substrate stacking position calculating apparatus calculates the positional relationship of two or more transparent substrates to be stacked when the two or more transparent substrates on which a plurality of lenses are two-dimensionally arranged are stacked to form a plurality of lens sets each including two or more lenses. A position of each lens is specified in advance in a common coordinate system.