In this paper, we study the second harmonic generation (SHG) from the stero-stacked meta-molecules consisting of two vertically stacked split ring resonators (SRRs) that resonate at the fundamental wavelength. When pumped by the linearly polarized incident wave with the electric field direction along one of the SRRs’ arms, the meta-molecules emit the SHG that can have two non-zero orthogonal electric field components, provided that the top SRR and the bottom SRR are not arranged in mutually parallel or anti-parallel manner. Due to the strong coupling between the two SRRs, the plasmonic properties of the stero-stacked meta-molecules could be tuned by varying the twist angle between the two SRRs. In this process, we demonstrate that the amplitudes of the two orthogonal SHG field components, and the phase difference between these two components can be varied with changing the twist angle between two SRRs. Based on the concept of the light polarization, different polarization states can be achieved by changing the differences in phase and amplitude between the orthogonal field components. Therefore, the twist angle dependent amplitudes of and phase difference between two orthogonal SHG field components can be used to manipulate the polarization states of the emitted SHG. For the stero-stacked meta-molecules with a fixed twist angle of 60°, elliptically, near-circularly andnear-linearly polarized SHG emission can be obtained at different fundamental wavelengths. In addition, for the fundamental wave with a fixed wavelength of 1500 nm, the stero-stacked meta-molecules with different twist angles are demonstrated to be able to emit SHG with elliptical andnear-linear polarization states.