Nano-precipitates of Guinier-Preston zones (or G.P. zones) occur in slowly cooled orthopyroxenes (OPX). Due to their nanometer sizes and intergrowth with host OPX, both X-ray diffraction and high-resolution TEM imaging cannot provide a consistent structure model for the G.P. zone precipitates. Combining Z-contrast imaging and density functional theory (DFT) methods, a correct crystal structure for the G.P. zone precipitates can be obtained, because Z-contrast imaging can reveal positions and occupancies of atoms directly. The crystal structure for the G.P. zone has P21/c symmetry with 4 types of tetrahedral chains (OA1, OA2, OB, OC). The structure can be considered as periodic stacking of half unit cells of enstatite sub-layers and of diopside sub-layers in a twinning-like relationship along a-axis. The G.P. zones that precipitate out from their host Ca-bearing OPX at low temperature are metastable with respect to end-members of enstatite and diopside.