Cancers heavily threaten human life, therefore, the high-accuracy diagnosis is vital to protect human beings from the suffer of cancers. While the biopsy and imaging methods have been widely used as current technologies for cancer diagnosis, new detection platform by metabolic analysis is expecting due to the significant advantages of fast, simple, and cost-effective with low body-intolerance. However, the signal of molecule biomarkers is too weak to acquire high-accuracy diagnosis. Herein, we developed precisely engineered metal-organic frameworks (MOFs) for laser desorption/ionization mass spectrometry (LDI MS), allowing favourable charge transfer within molecule-substrate interface and mitigated thermal dissipation by adjusting the phonon scattering with metal nodes. Consequently, we achieved a surprising signal enhancement of ∼10,000-fold, resulting in diagnosis of three major cancers (liver/lung/kidney cancer) with area-under-the-curve (AUC) of 0.908-0.964 and accuracy of 83.2%-90.6%, which promises a universal detection tool for large-scale clinical diagnosis of human cancers. This article is protected by copyright. All rights reserved