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Quantum key distribution (QKD) has attracted much attention due to its unconditional security. High-dimensional quantum key distribution (HD-QKD) is a brand-new type of QKD protocol that has many excellent advantages. Nonetheless, practical imperfections in realistic devices that are not considered in the theoretical security proof may have an impact on the practical security of realistic HD-QKD systems. In this paper, we research the influence of a realistic intensity modulator on the practical security of HD-QKD systems with the decoy-state method and finite-key effects. We demonstrate that there is a certain impact in the secret key rate and the transmission distance when taking practical factors into security analysis.