The enhanced infrared absorbance (IRA) of the complementary metal-oxide-semiconductor (CMOS) compatible thermopile with the subwavelength rectangular-hole arrays in active area is investigated. The finite-difference time-domain (FDTD) method considered and analyzed the matrix arrangement (MA) and staggered arrangement (SA) of subwavelength rectangular-hole arrays (SRHA). For the better cases of MA-SRHA and SA-SRHA, the geometric parameters are the same and the infrared absorption efficiency (IAE) of the SA type is better than that of the MA type by about 19.4% at target temperature of 60 °C. Three proposed thermopiles with SA-SRHA are manufactured based on the 0.35 μm 2P4M CMOS-MEMS process. The measurement results are similar to the simulation results. The IAE of the best simulation case of SA-SRHA is up to 3.3 times higher than that without structure at the target temperature of 60 °C. Obviously, the staggered rectangular-hole arrays with more appropriate geometric conditions obtained from FDTD simulation can excellently enhance the IRA of the CMOS compatible thermopile.