Information on isotopic composition and geometric structure is necessary for identifying a true warhead. Nevertheless, such classified information should be protected physically or electronically. With a novel Hash encryption algorithm, this paper presents a Monte Carlo-based design of a neutron activation analysis verification module. The verification module employs a thermal neutron source, a non-uniform mask (physically encrypting information about isotopic composition and geometric structure), a gamma detector array, and a Hash encryption algorithm (for electronic encryption). In the physical field, a non-uniform mask is designed to distort the characteristic gamma rays emitted by the inspected item. Furthermore, as part of the Hash algorithm, a key is introduced to encrypt the data and improve the system resolution through electronic design. In order to quantify the difference between items, Hamming distance is used, which allows data encryption and analysis simultaneously. Simulated inspections of simple objects are used to quantify system performance. It is demonstrated that the method retains superior resolution even with 1% noise level. And the performances of anti-statistical attack and anti-brute force cracking are evaluated and found to be very excellent. The verification method lays a solid foundation for nuclear disarmament verification in the upcoming era.