BackgroundIsomaltulose is a ‘generally recognized as safe’ ingredient and is widely used in food, pharmaceutical and chemical industries. Exploration and development of efficient technologies are essential for enhancing isomaltulose yield.ResultsIn this study, a simple and efficient surface display platform mediated by a non‐yeast signal peptide was developed in Yarrowia lipolytica and was utilized to efficiently produce isomaltulose from sucrose. We discovered that the signal peptide SP1 of sucrose isomerase from Pantoea dispersa UQ68J (PdSI) could guide SIs anchoring to the cell surface of Y. lipolytica, demonstrating a novel and simple cell surface display strategy. Furthermore, the PdSI expression level was significantly increased through optimizing the promoters and multi‐site integrating genes into chromosome. The final strain gained 451.7 g L−1 isomaltulose with conversion rate of 90.3% and space–time yield of 50.2 g L−1 h−1.ConclusionThis study provided an efficient way for manufacturing isomaltulose with high space–time yield. This heterogenous signal peptide‐mediated cell surface display strategy featured with small fusion tag (~2.2 kDa of SP1), absence of enzyme leakage in fermentation broth, and ample room for optimization, providing a convenient way to construct whole‐cell biocatalysts to synthesize other products and broadening the array of molecular toolboxes accessible for engineering Y. lipolytica.This article is protected by copyright. All rights reserved.