An electrical isolator packaging structure and a manufacturing method of an electrical isolator are provided. The electrical isolator packaging structure includes a first substrate, a second substrate, a coil, and a magnetic field (MF) sensor. The coil is disposed on the first substrate. The MF sensor is disposed on the second substrate. The position of the coil is arranged according to the position of the MF sensor such that the coil transmits a signal to the MF sensor. Thus, the electrical isolator can be implemented by magnetic coupling with the coil and the MF sensor.