Microscale liquid crystal thermography is a technique to measure temperature distribution of microfabricated devices in real-time. This method utilizes a microscope to image the color map of a layer of temperature-sensitive encapsulated thermochromic liquid crystals (TLC) coated on a microfabricated device. This paper describes the TLC coating process on microscale devices, the characteristics of colorimetric hysteresis, and the calibration of temperature measurements. The calibrated measurements have been applied for characterization of an on-chip polymerase chain reaction (PCR) microscale thermocycler where precise and dynamic temperature control is essential for efficient DNA amplification. Tests on the micro-thermocycler were done around the ranges centered at 30°C and 95°C. The results illustrate the effects on the temperature distribution due to micro-thermocycler geometry, and provide important insight for micro-thermocycler design.