A novel direct method of micro/nano quantum dot (QD) patterning via one-step imprinting over a large area at low temperatures and low pressures was demonstrated as an alternative to conventional vacuum deposition and photolithography methods. More complex QD patterning could be demonstrated by expanding the QD direct imprinting process for multiple colored QD and patterning on the multiple layers. Additionally, a self-alignment scheme was developed to pattern multiple layers without the need for laborious alignment steps. Our approach may be useful for QD-based optoelectronic device fabrication and patterning on large flexible substrates due to the low-temperature requirements of this process.