Paramagnetic LaNiO (LNO)-based heterostructures have been attracting the attention of researches, especially since the interesting exchange bias (EB) effect has been observed in (111)-oriented LaMnO (LMO)/LNO superlattices (SLs). However, this effect is not expected to occur in the (001) direction SLs. In this paper, we report the observation of an unexpected EB effect in (001)-oriented (LMO)/(LNO) SLs. The orbits of interfacial Mn/Ni ions preferentially occupy the strain-stabilized x - y in ultrathin LNO layers [t ≤ 4 unit cells (u.c.)]. Conversely, as the LNO layer becomes thicker (t ≥ 6 u.c.), the EB effect is absent, and the orbits are reconstructed to form the 3z - r preferential occupancy. The absence of the EB in thicker LNO-based SLs is attributed to the interfacial charge transfer suppressed by orbital reconstruction as a consequence of the increasing LNO thickness. In the thinner LNO-based SLs, the larger charge transfer results in stronger localized magnetic moments for the cause of the EB effect. These results provide a useful interpretation of the relationship between macroscopic magnetic properties and the microscopic electronic structure in oxide-based heterostructures.