A light sensing packaging structure and a packaging method thereof is provided, wherein the light sensing packaging structure comprises a substrate provided with a through-hole between a light-emitting element and a light-sensing element; and a cover body covered the substrate. The cover body comprises a shielding part and an extended part. The shielding part is mounted between the light-emitting element and the light-sensing element, and provided with a metal bonding layer on a surface towards the substrate. The extended part is provided with a metal side wall connected to the metal bonding layer. The through-hole is covered with a conductive glue, and the metal junction contacts the conductive glue. Hereby, the present application may reduce the size of the light sensing device, provide a stable packaging, reduce the packaging cost and improve the reliability of the light sensing product.