Effective detection of bio‐molecules relies on the precise design and preparation of materials, particularly in laser desorption/ionization mass spectrometry (LDI‐MS). Despite significant advancements in substrate materials, the performance of single‐structured substrates remains suboptimal for LDI‐MS analysis of complex systems. Herein, we develop designer Au@SiO2@ZrO2 core‐shell substrates for LDI‐MS‐based early diagnosis and prognosis of pancreatic cancer (PC). Through controlling Au core size and ZrO2 shell crystallization, we not only achieved signal amplification of metabolites up to 3 orders but also revealed the synergistic mechanism of the LDI process. The optimized Au@SiO2@ZrO2 enables a direct record of serum metabolic fingerprints (SMFs) by LDI‐MS. Subsequently, we employed SMFs to distinguish early PC (stage I/II) from controls, with an accuracy of 92%. Moreover, we established a prognostic prediction scoring system with enhanced efficacy in predicting PC survival compared to CA19‐9 (p < 0.05). Our work contributes to material‐based cancer diagnosis and prognosis.This article is protected by copyright. All rights reserved