Micropatterning of quantum dot (QD)-polymer nanocomposites exhibiting optically and electrically programmable properties in a large area with an organized array has been of great importance in various applications using photonic and optoelectronic devices. Here, we report the fabrication of a micropatterned QD-polymer composite exhibiting superior photoluminescence (PL) properties employing thiol-ene reaction and imprinting lithography techniques. The presence of positive charge on the QDs enhances the dispersion interaction between the QDs, and the presence of positively charged QDs containing allylic groups enables the QDs to form strong chemical binding to the polymer matrix. This phenomenon was confirmed using three different QDs; a neutral QD (QD-TOH), positive QD (QD-TTMA), and positive QD containing allylic groups (QD-TDMA–Ene). The synergetic effect of charge repulsion and chemical binding observed in our system induces a high PL with robustness of micropatterns. Moreover, the PL intensity linearly depends on the QD content in the polymer matrix, indicating easy controllability of the system, which can be used as a light-emitting source.