Due to the high single-photon detection sensitivity and the characteristics of multiple pixels, single-photon detector arrays (SPDA) have been widely applied in the areas of single-photon radar, bioluminescence imaging, and so on. However, limited by fabrication technology, the photon detection efficiency of each pixel of SPDA presents a certain difference, which often leads to imaging distortion. To solve this problem, the reverse bias voltage of each single photon detector for a 4 × 4 SPDA has been optimized individually in this work, which increases the averaged photon detector efficiency by 1.77 folds and reduces the difference to 1/7 of that before adjustment. Then on this basis, a Fourier-domain imaging (FDI) scheme has been developed by performing Fourier transform on the photon arriving time of each single-photon detector and using Fourier transform amplitude as the imaging parameter. The results show that with FDI scheme, a reasonably good imaging with a contrast-to-noise ratio up to 2.29 can still be determined even under the condition that the ratio of the noise intensity to the signal intensity reaches 104, manifesting the strong noise-resistant feature of FDI. This work offers a new route for achieving single photon detector under complex and noisy environments based on SPDA.