A manufacturing method of chip package structure includes following steps. A carrier is provided. A first patterned circuit layer and a first dielectric layer covering the first patterned circuit layer have been formed on the carrier. A flat structure layer is formed on the first dielectric layer. A second dielectric layer is formed on the first dielectric layer and covers the flat structure layer and a portion of the first dielectric layer. A second patterned circuit layer is formed on the second dielectric layer. The second patterned circuit layer includes a plurality of pads. An orthographic projection of the flat structure layer on the carrier overlaps orthographic projections of the pads on the carrier. A plurality of chips are disposed on the pads. A molding compound is formed to cover the second dielectric layer and encapsulate the chips and the pads.