Abstract: To address the problems of poor directionality and limited detection distance in the remote localization of micro-leaks inside large-scale vacuum vessels, a directional molecular-flow detection method based on the coupling of a multi-capillary array and a mechanical chopper wheel is proposed. A theoretical model for the transport of leaked gas through the multi-capillary array under molecular-flow conditions was established. The effects of capillary length-to-diameter ratio, array conductance, and system response time on the detected signal were analyzed. The method was further verified by COMSOL and Molflow simulations as well as vacuum-chamber scanning experiments. The simulation and experimental results show that the multi-capillary array can significantly enhance the pressure signal of the leaked gas, and the signal enhancement increases with the length-to-diameter ratio of the capillaries. At the same detection distance, the array with d = 2 mm and l = 30 mm exhibits a stronger detection signal than the array with d = 2.5 mm and l = 20 mm. The experimentally measured maximum detectable distances of the two arrays are 115 mm and 92 mm, respectively, which are in good agreement with the theoretical calculations. The mechanical chopper wheel can realize periodic modulation of the leakage signal. When the rotational speed is 0.125–0.25 r/s, the modulated signal matches well with the system response time. The results indicate that the proposed method can be applied to remote directional detection of micro-leaks inside vacuum vessels and provides a new technical approach for long-distance and high-efficiency localization of micro-leaks in large-scale vacuum vessels.