A novel electromagnetic heat method is presented for green extraction of natural compounds from peel residue. In the processing cavity obtained through 3D printing, a core made of amorphous alloy was applied to strengthen the magnetic flux. During the process, an induced electric field was produced in the extract medium owing to an oscillating magnetic field at 50 kHz rather than a pair of electrodes; thus, electrochemical reactions could be avoided. A thermal effect and temperature rise were observed under the field, and essential oil was obtained via this electromagnetic heat hydrodistillation. In addition, the numerical relationships between magnetic field, induced electric field (IEF), induced current density, and temperature profile were elaborated; they were positively correlated with the extraction yield of essential oils. It was found that the waveforms of the magnetic field, induced electric field, and excitation voltage were not consistent. Using a higher magnetic field resulted in high current densities and terminal temperatures in the extracts, as well as higher essential oil yields. When the magnetic field strength was 1.39 T and the extraction time was 60 min, the maximum yield of essential oil reached 1.88%. Meanwhile, conventional hydrodistillation and ohmic heating hydrodistillation were conducted for the comparison; all treatments had no significant impact on the densities. In addition, the essential oil extracted by electromagnetic heat had the lowest acid value and highest saponification value. The proportion of monoterpenoids and oxygen-containing compounds of essential oil extracted by this proposed method was higher than the other two methods. In the end, the development of this electromagnetic heat originating from magnetic energy has the potential to recover high-value compounds from biomass waste.