An electron bombarded active pixel sensor (EBAPS) is a novel vacuum-solid, hybrid, digital, low-light night vision device. Flicker noise is a key factor affecting the resolution and image quality of EBAPS; however, there is currently insufficient research on the testing of flicker noise in EBAPS. Hence, this study conducted research on EBAPS flicker noise testing methods using connected domain detection algorithms to filter out high-brightness noise spot areas and proposed an adaptive, median replacement, discrete coefficient testing method for abnormal pixel points. Based on these results, an EBAPS flicker-noise testing system was developed using the discrete coefficient and number of bright noise spots as parameters to characterize the flicker noise. The system drives the EBAPS to transfer image data collected under different test conditions to an upper computer for noise processing and analysis. The test results indicate that the appropriate test illuminance is 1.27×10⁻³ lx. Moreover, the number of high-brightness noise spots is relatively low in the −1000−1300 V range, and it significantly increases when the voltage is between −1300−1500 V. The repeatability of the discrete coefficient and number of connected domains was within 3%, thus verifying the stability of the testing system and providing an effective means by which to test flicker noise in domestic EBAPS.