A heat sink protective cover includes a main body, on which at least one receiving space is defined for receiving a heat sink therein. The receiving space includes at least one positioning section and a dust-proof section. The positioning section is located at two opposite inner wall surfaces of the receiving space. The dust-proof section includes a raised portion and a recess portion, the raised portion is extended along a periphery of the dust-proof section to limit the recess portion on four sides thereof, and the dust-proof section is located on a bottom of the receiving space. The heat sink is stably hold in place in the receiving space by the positioning section and isolated from dust by the dust-proof section, and can therefore be effectively protected against collision, damage, and contamination while being transported.