It is challenging to rational design persistent luminescence and storage phosphors with high storage capacity of electrons and holes after X-ray charging. Such phosphors have potential applications in anti-counterfeiting and X-ray imaging. Here we have combined vacuum referred binding energy diagram (VRBE) construction, photoluminescence spectroscopy, and thermoluminescence to study the trapping processes of charge carriers in NaYGeO₄. In NaYGeO₄:0.004Bi³⁺ and NaYGeO₄:0.004Bi³⁺,0.005Ln³⁺ (Ln = Tb or Pr), Bi³⁺ appears to act as a shallow electron trap, while Bi³⁺ and Ln³⁺ act as deep hole trapping and recombination centres. We will show how to experimentally determine the VRBE in the Bi^{2+ 2}P_1/2 ground state in NaYGeO₄ and NaLuGeO₄ by thermoluminescence study. The electron trap depth produced by Bi³⁺ codopant in NaLu_1-xY_xGeO₄:0.003Bi³⁺,0.008 Tb³⁺ can be adjusted, by increasing x, resulting in conduction band engineering. By combining Bi³⁺ as an electron trap and Bi³⁺ and Tb³⁺ as the hole traps, excellent X-ray charged afterglow phosphors were developed. The integrated TL intensity of the optimized NaYGeO₄:0.004Bi³⁺ and NaYGeO₄:0.003Bi³⁺,0.008Tb³⁺ after exposure to X-rays is about 4.5 and 1.1 times higher than that of the state-of-the-art BaFBr(I):Eu²⁺ storage phosphor. Intense initial Tb³⁺ 4f → 4f afterglow appears in NaYGeO₄:0.003Bi³⁺,0.008Tb³⁺ and more than 40 h afterglow is measurable in NaYGeO₄:0.004Bi³⁺ and NaYGeO₄:0.003Bi³⁺, 0.008 Tb³⁺ after X-ray charging. We will show proof-of-concept anti-counterfeiting and X-ray imaging applications by using the developed afterglow phosphors and CsPbI₃ quantum dots. This work not only provides experimental evidence on the VRBE in the Bi^{2+ 2}P_1/2 ground state in NaYGeO₄, but also shows how to design and develop good afterglow phosphors for anti-counterfeiting and X-ray imaging by deeply studying and controlling the trapping processes of charge carriers in bismuth and/or lanthanides doped inorganic compounds.