A method for forming a three-dimensional memory device includes forming, on a first side of a first substrate, a plurality of semiconductor device arrays and forming a first interconnect layer on the plurality of semiconductor device arrays. The method also includes forming, on a second substrate, a memory array including a plurality of memory cells and a second interconnect layer. The method further includes bonding the first and second interconnect layers and forming one or more isolation trenches through a second side of the first substrate that is opposite to the first side to expose a portion of the first side of the first substrate. The one or more isolation trenches are formed between first and second semiconductor device arrays of the plurality of semiconductor devices arrays. The method further includes disposing an isolation material to form one or more isolation structures respectively in the one or more isolation trenches.