Mid-wavelength infrared (MWIR) HgCdTe electron-initiated avalanche photodiodes (e-APDs) have presented excellent performances to resolve and count photons with linear mode. Aiming at low flux, the ROIC noise can be extremely reduced by certain gain, and very low excess noise makes opportunity for noise equivalent photon (NEPh) to be 1. Therefore, the main issue for SNR of HgCdTe APD is gain normalized dark current density (GNDCD) at high reverse bias. In this work, the architecture of multiplication region is modeled and studied. The depth and width of multiplication region are controlled by regulating the p-type doping concentration, ion implantation and post thermal annealing conditions as well. Proper processes can keep the peak electric field away from the implantation damage region, effectively increase the Shockley–Read–Hall (SRH) lifetime, reduce the multiplication region concentration and finally increase the operating voltage. Considered with dark current and gain, depletion region (I region) width is optimized and characterized to be 3–3.6 μm when I region concentration is ∼1 × 1015 cm−3 in our case. The GNDCD of MW APD (cut off wavelength ∼5.16 μm @80 k) is less than 10−6 A/cm2@≤-10 V, with avalanche gain of ∼1570@-9.8 V. The excess noise factor (F) is measured to be 1–1.4 by noise power spectral density (PSD). The NEPh value is less than 5 photons with gain up to ∼280 for MW 128 × 128 HgCdTe APD array. Simulation results anticipate that GNDCD can be further reduced by decreasing the doping concentration of I region to below 5 × 1014 cm−3. Furthermore, increasing the p-type doping concentration and band gap will significantly reduce GNDCD below to ∼10−10 A/cm2@-10 V for 4.22 μm Hg1-xCdxTe (x = 0.332) APD.