The interfaces between organic molecules and magnetic metals have gained increasing interest for both fundamental reasons and applications. Among them, the C/layered antiferromagnetic (AFM) interfaces have been studied only for C bonded to the outermost ferromagnetic layer [S. L. Kawahara et al., Nano Lett. 12, 4558 (2012) and D. Li et al., Phys. Rev. B 93, 085425 (2016)]. Here, via density functional theory calculations combined with evidence from the literature, we demonstrate that C adsorption can reconstruct the layered-AFM Cr(001) surface at elevated annealing temperatures so that C bonds to both the outermost and the subsurface Cr layers in opposite spin directions. Surface reconstruction drastically changes the adsorbed molecule spintronic properties: (1) the spin-split p-d hybridization involves multi-orbitals of C and top two layers of Cr with opposite spin-polarization, (2) the subsurface Cr atom dominates the C electronic properties, and (3) the reconstruction induces a large magnetic moment of 0.58 μ in C as a synergistic effect of the top two Cr layers. The induced magnetic moment in C can be explained by the magnetic direct-exchange mechanism, which can be generalized to other C/magnetic metal systems. Understanding these complex hybridization behaviors is a crucial step for molecular spintronic applications.