We report an unexplored observation of multi-orbital contribution in the below- and near-threshold harmonic generation of aligned molecules. The typical pump-probe configuration is used in our experiments. By scanning the time delay and crossing angle of polarization directions between the pump and probe pulses, we find that the harmonic yield in this region exhibits abnormal intensity-dependent modulation patterns. Further comparison and analysis show that this observation can be interpreted by the contribution of deeper-lying molecular orbitals, which is much more prominent than in the above-threshold region and can overall surpass the contribution of the highest occupied molecular orbital, leading to reversed modulation patterns. The particular importance of the deeper-lying orbitals in this regime is closely related to the multi-photon excitation pathways involved in the generation process. Our work will advance further investigations on the mechanism of the below- and near-threshold harmonic generation.