Due to its advantages of uncooling, ease of operation and low cost, micromachined thermopile infrared (IR) detectors have a broad application. A novel complementary metal-oxide-semiconductor (CMOS) compatible self-aligned micromachined thermopile IR detector is proposed to reduce the fabrication complication and fabrication difficulty of micro etching windows. Compared with conventional micromachined thermopile IR detectors, the etching windows in the self-aligned thermopile structure are determined by space between polysilicon thermocouple legs rather than by photolithographic processing. Two types of thermopile structures are designed and fabricated in order to study the influence of device structure on IR detector performance. Experimental results show that the rectangular thermopile structure has a higher output voltage and responsivity, whereas the circular IR detector exhibits a smaller response time and a higher specific detectivity.