Three-dimensional memory device containing self-aligned bit line contacts and methods for forming the same

A vertical layer stack including a bit-line-level dielectric layer and an etch stop dielectric layer can be formed over an array region. Bit-line trenches are formed through the vertical layer stack. Bit-line-trench fill structures are formed in the bit-line trenches. Each of the bit-line-trench fill structures includes a stack of a bit line and a capping dielectric strip. At least one via-level dielectric layer can be formed over the vertical layer stack. A bit-line-contact via cavity can be formed through the at least one via-level dielectric layer and one of the capping dielectric strips. A bit-line-contact via structure formed in the bit-line-contact via cavity includes a stepped bottom surface including a top surface of one of the bit lines, a sidewall segment of the etch stop dielectric layer, and a segment of a top surface of the etch stop dielectric layer.