Public places, such as airports, factories, public institutions, and organizations, require advanced security measures. X-Ray systems are often used to check passengers' luggage. Researchers and technologists are constantly working to improve the baggage-checking process by implementing various methods. This study introduces a new method for estimating the effective atomic number. Traditionally, effective atomic number estimation relies on the ratio between high-energy and low-energy images. However, the 3D Effective Atomic Number Estimation model uses high-energy and low-energy image values directly, resolving many issues of the 1D-Ratio model.