We describe a high-throughput synthesis of multi-colored emissive microstructure with rare-earth doped upconverting nanocrystals (UCNs) using a contact flow lithography. UCNs have the optical specificity of anti-stoke effect that absorb near infrared rays (NIR) and emit visible light. However, most upconversion nanocrystals should control the concentration of lanthanide dopant very precisely to manipulate the emission color. Herein, we suggest a method of microstructure synthesis which has a variety of shapes and multiple luminescence color through applying contact flow lithography technique to luminescence property of UCNs. Our results have great advantages of being applicable to an anti-counterfeiting technology and encoding system.