An infrared thermopile sensor includes a silicon cover having an infrared lens, an infrared sensing chip having duo-thermopile sensing elements, and a microcontroller chip calculating a temperature of an object. The components are in a stacked 3D package to decrease the size of the infrared thermopile sensor. The infrared sensing chip and the microcontroller chip have metal layers to shield the thermal radiation. To measure object temperature accurately under acute change in environmental temperature, this disclosure uses the duo-thermopile sensing elements, that one is the active unit for measuring the object temperature and another one is the dummy unit for compensating the effect from the package structure.