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We present a novel approach to achieve spatial variations in the degree of non-covalent functionalization of twisted bilayer graphene (tBLG). The tBLG with twist angles varying between ~ 5{\deg} and 7{\deg} was non-covalently functionalized with 1,4,5,8,9,11-hexaazatriphenylenehexacarbonitrile (HATCN) molecules. Our results show a correlation between the degree of functionalization and the twist angle of tBLG. This correlation was determined through Raman spectroscopy, where areas with larger twist angles exhibited a lower HATCN peak intensity compared to areas with smaller twist angles. We suggest that the HATCN adsorption follows the moir\'e pattern of tBLG by avoiding AA-stacked areas and attach predominantly to areas with a local AB-stacking order of tBLG, forming an overall ABA-stacking configuration. This is supported by density functional theory (DFT) calculations. Our work highlights the role of the moir\'e lattice in controlling the non-covalent functionalization of tBLG. Our approach can be generalized for designing nanoscale patterns on two-dimensional (2D) materials using moir\'e structures as a template.