The chemical composition of the deep continental crust is key to understanding the formation and evolution of the continental crust. However, constraining the chemical composition of deep continental crust is limited by indirect accessibility. Here we present a modeling method to constrain deep crustal chemical structures from observed crustal seismic structures. We first compile a set of published composition models for the continental crust. Phase equilibria and compressional wave speeds (VP) are calculated for each composition model at a range of pressure and temperature (278–2223 MPa, 50–1200°C). Functional relationships are obtained between calculated wave speeds and crustal compositions at pressure and temperature conditions within the alpha(α)-quartz stability field. These relationships can invert observed seismic wave speeds of the deep crust to chemical compositions in regions with given geotherms (MATLAB code is provided). We apply these relationships to wave speed constraints of typical tectonic settings of the global continental crust and the North China Craton. Our method predicts that the lower crust in regions with thin- (e.g., rifted margins, rifts, extensional settings, and forearcs) or thick-crust (e.g., contractional orogens) is more mafic than previously estimated. The difference is largest in extensional settings (52.47 ± 1.18 and 51.11 ± 1.61 vs. 59.37 wt. % SiO2). The obtained 2-D chemical structure of the North China Craton further shows features consistent with the regional tectonic evolution history and xenoliths. The obtained chemical structure can serve as a reference model from which chemical features in the deep crust can be recognized.