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This study investigated the formation and molecular interaction mechanism of chestnut starch nanocrystal (SNC)/macadamia protein isolate (MPI) complexes and their application in edible oil-in-water Pickering emulsion (PE). SNC/MPI complexes were characterized by scanning electron microscopy and particle size analyzer. The PEs stabilized by SNC/MPI complexes were characterized by confocal laser scanning microscopy and rheological measurement. The results showed that hydrogen bonds between the two particles significantly affected the secondary structure and assembly of SNC/MPI complexes at the oil/water interface. The optimal mass ratio of SNC to MPI in the complexes with the best stability was determined as 20:1. The formation of edible oil-in-water PEs stabilized by SNC/MPI complexes significantly improved the oxidative and storage stability of different edible oils (olive oil, walnut oil, edible tea oil, and macadamia oil). These different edible oil-in-water PEs stabilized by SNC/MPI could be used as effective carriers of quercetin with their loading rates higher than 93%.