A wiping mechanism is provided for wiping a substrate during transmission. The wiping mechanism comprises an upper wiping unit and a lower wiping unit moving back and forth for separately wiping an upper side and a lower side of the substrate. The moving directions of the upper wiping unit and the lower wiping unit are parallel to a loading plane for disposing the substrate and vertical to a transmission direction of the substrate, and the moving directions of the upper wiping unit and the lower wiping unit are opposite to each other, thereby to prevent the substrate being shifted due to wiping, to guarantee the effect of cleaning foreign particles from the surface of the substrate and to avoid scratching the surface of the substrate, to prevent the cleaning apparatus from being damaged, and to avoid affecting the substrate transmission. A substrate cleaning apparatus is also provided.