The detection of cations plays a significant role in environmental, pharmaceutical, and clinical analysis. In this study, a uniform Au nanoparticle/PbSe quantum dot heterostructure that promotes the desorption of a variety of cationic analytes (e.g., malachite green, berberine, and choline) was designed based on a layer-by-layer assembly strategy. The fabrication process involved applying a monolayer of AuNPs to a derivatized coverslip, followed by depositing a second layer of PbSe QDs. Through ultraviolet− visible−near-infrared spectroscopy, X-ray photoelectron spectroscopy, Raman spectroscopy, and Hall effect measurements, it was revealed that the oxidation of PbSe QDs can induce a transition in electrical transport from n-type to p-type conductivity. This significant change results in an Ohmic contact formed at the heterointerface, which facilitates the transfer of holes from the underlying AuNPs to the surface of PbSe QDs upon UV laser excitation. Thus, the accumulated holes of QDs repel the cationic analytes via Coulombic forces, significantly enhancing the desorption process on the Au/PbSe heterostructure compared to that of the reverse layer configuration. The enhancement in desorption is not attributed to thermal effects, as further confirmed by employing benzylpyridinium as a chemical thermometer. Finally, this hole-driven substrate was applied to quantify choline levels in the human serum from healthy controls and lung cancer patients, and it had high sensitivity and linear correlation for real samples. The results demonstrated that Au/PbSe-assisted LDI-MS offers significant advantages in rapid cation screening and biomedical diagnostics.