The invention relates to a single-chip flip, etching-after-packaging and pad embedded packaging structure and a manufacturing method thereof. The structure comprises pads (1), pins (2) and a chip (3). The chip is arranged on the right sides of the pads and the pins in an inverted mode; bottom filling glue (14) is arranged between the bottom of the chip and the right sides of the pads and the pins; molding compounds (4) are packaged in areas on the peripheries of the pads, between the pads and the pins, among the pins, on the upper portions of the pads and the pins, on the lower portions of the pads and the pins and on the periphery of the chip; holes (5) are opened on the molding compounds on the reverse sides of the pins, and communicated with the reverse sides of the pins; and metal balls (7) are arranged in the holes and contacted with the reverse sides of the pins. The single-chip flip, etching-after-packaging and pad embedded packaging structure and the manufacturing method thereof have the advantages of reducing manufacturing costs, improving safety and reliability of packaging bodies, reducing environmental pollution, and being capable of designing and manufacturing high-density lines.