Chiral nanomaterials offer intriguing possibilities for novel electronic and chemical applications. Here, we report the discovery of an enantiomer-selective magnetoresistance effect in chiral gold nanocrystals. Based on precise control of nanocrystal chiral morphology using amino acid-directed synthesis, we demonstrate that an external magnetic field can dramatically modulate resistance in an enantiomer-specific manner. For a given enantiomer, a magnetic field in one direction alters the resistance by over an order of magnitude, while the opposite field direction leaves it unchanged. This asymmetric response reverses for the opposite enantiomer. We attribute this phenomenon to a novel chirality-driven charge trapping mechanism, where the interplay between the chiral nanocrystal morphology and the magnetic field selectively modifies the surface potential. The magnitude and sign of the magnetoresistance can be further tuned by the surface chemistry of the nanocrystal, as demonstrated through sulfide treatment. Our findings reveal a new form of chirality-dependent magnetoresistance, distinct from previously known effects such as chirality-induced spin selectivity and electric magnetochiral anisotropy. The ability to remotely control surface potentials of chiral nanostructures using magnetic fields could enable novel approaches in catalysis, drug delivery, and nanoelectronics.