This paper systematically investigates the conducted electromagnetic interference (EMI) using separated heat sinks for a silicon carbide (SiC) JFET inverter for motor drives. The inverter circuit layout is implemented with discrete SiC JFETs attached on top of the heat sink, which creates extensive capacitive couplings and moreover increases parasitic oscillations. To minimize the influence, the solution of using separated heat sinks is proposed. For better common mode performance, the high-side heat sink is grounded to avoid fast dv/dts that occur between the drain of the lower switch and the low-side heat sink. For better differential mode performance, the RC snubber circuit and ferrite beads are used to damp parasitic oscillations. Two 2.2 kW inverter prototypes, with six discrete SiC JFETs on one common heat sink and separated heat sinks, respectively, are built using the same circuit layout. Their EMI spectra are compared under unfiltered and filtered conditions. The experiments show that the separate heat sinks inverter system exhibits significantly reduced EMI. Last, three improved solutions are proposed, which effectively suppresses the emitted EMI to the target level.