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In order to increase the concentrations of bio-based alkyd polyols (or fatty acids) in self-crosslinking polyurethane dispersions, herein, a series of novel alkyd polyol-based autoxidizable waterborne polyurethane dispersions (AWPUDs) with different fatty acid contents, long storage stability, and low viscosity were successfully prepared by adding dimethylol propionic acid (DMPA) self-emulsifier in the late stage of their synthesis. They and their corresponding curing films were characterized by Fourier transform infrared spectroscopy (FTIR), particle size analysis, rheology measurement, storage stability evaluation, thermogravimetric analysis, dynamic thermomechanical analysis (DMA), etc. The results showed that the addition process of DMPA played a critical role for the excellent features of AWPUDs. Additionally, the crosslinking density, gel contents, and water contact angles of AWPUD films increased with the enlarged fatty acid contents, whereas their water uptake capability decreased. Moreover, a series of AWPUD coatings were prepared, and their properties like drying times, hardness development, pencil hardness, adhesion capability, impact resistance, flexibility, and water resistances were all effectively improved with the increased fatty acid contents, significantly superior to those of waterborne alkyd coatings and waterborne polyurethane coatings without fatty acids.