An integrated circuit (IC) packaging substrate includes a main body, at least one first conductive line, at least one second conductive line, and at least one protrusion pad. The first conductive line is embedded in the main body. The second conductive line is embedded in the main body. The protrusion pad is disposed on the first conductive line. The protrusion pad protrudes from the main body and is configured to be in electrical contact with a solder portion of a semiconductor chip. A first spacing between the protrusion pad and the second conductive line is determined in accordance with a process deviation of the protrusion pad by the width of the protrusion pad and the width of the first conductive line. Moreover, a semiconductor package having the IC packaging substrate and a manufacturing method of the semiconductor package are also provided.