The influence of the varied thickness of antiferromagnetic (AFM) and ferrimagnetic (FiM) nanostructure in MnO@Mn3O4 core-shell nanoparticles (NPs) on the exchange bias effect has been investigated. The MnO@Mn3O4 core-shell NPs with varied radius of MnO core (RMnO) and thickness of Mn3O4 shell (TMn3O4) have been synthesized by in-situ oxidation of the pure MnO NPs in organic solution containing a mild oxidant at different temperatures. The exchange bias effect can be tuned by changing the RMnO (TMn3O4) of the MnO@Mn3O4 core-shell NPs. The strongest exchange coupling effect of both 17.2 and 25.0 nm MnO@Mn3O4 core-shell NPs occur when RMnO=TMn3O4=R/2. It is expected that the finding of the control of exchange bias effect by varied RMnO and TMn3O4 in inverted core-shell NPs is helpful for the further understanding of the exchange bias mechanism.