In an energy subtraction processing apparatus, method, and a non-transitory computer readable recording medium storing program, a high-quality image is generated by acquiring an absorption coefficient suitable for a subject. A subject information acquisition unit acquires the thickness information of a breast and a mammary gland content rate, as subject information, based on a low voltage image acquired by energy subtraction imaging. An absorption coefficient acquisition unit acquires an absorption coefficient corresponding to the subject information with reference to the relationship between the thickness of the breast and the X-ray absorption coefficient, which is calculated in advance. Based on the absorption coefficient acquired by the absorption coefficient acquisition unit, a weighting coefficient calculation unit calculates a weighting coefficient at the time of performing energy subtraction processing. A subtraction unit performs subtraction processing using the weighting coefficient calculated by the weighting coefficient calculation unit.