The present disclosure provides a packaging assembly and a manufacturing method thereof. The packaging assembly comprising a first substrate, a second substrate arranged opposite to the first substrate, an electronic device located between the first substrate and the second substrate, a protective layer covering the electronic device, and a bonding layer for bonding the first substrate and the second substrate so as to realize surface-to-surface packaging. The packaging assembly further comprising an isolation layer located between the bonding layer and the protective layer and adhered to both them, wherein an adhesion force between the material for forming the isolation layer and that for forming the bonding layer is smaller than an adhesion force between the material for forming the protective layer and that for forming the bonding layer.