A method of manufacturing a three-dimensional integrated circuit structure includes the following steps. A first die is provided. A plurality of second dies are bonded onto the first die, wherein a gap is formed between the plurality of second dies. A dielectric material is filled in the gap by performing at least one cycle of: by a first deposition process, forming a first dielectric layer having a smaller thickness at a top portion of a sidewall of the gap than a bottom portion of the sidewall of the gap; and by a second deposition process, forming a second dielectric layer on the first dielectric layer over the gap. A portion of the dielectric material is removed to form a dielectric structure between the plurality of second dies, wherein a top surface of the dielectric structure is substantially coplanar with tops surfaces of the plurality of second dies.