The magnetic nylon-6 short fiber is made with magnetic functional agglomerate and nylon chip in the weight ratio of 1 to 5-10. The magnetic functional agglomerate includes functional powder, carrier chip, dispersant, coupler and antioxidant in certain weight proportion. The making process of the magnetic nylon-6 short fiber includes the following steps: 1. preparing the magnetic functional agglomerate through preparing functional powder of Fe3O4, drying and activating the functional powder, mixing the functional powder with carrier chip, dispersant, coupler and antioxidant in certain weight proportion via high speed stirring, cooling the mixture to room temperature, and extruding and pelletizing in extruder; and 2. producing magnetic nylon-6 short fiber through mixing magnetic functional agglomerate and nylon chip, spinning the mixture, winding, bundling, drafting, dewatering, crimping, setting and cutting.