Bio‐based polyols derived from vegetable oils generally contain the dangling chains, which have recently attracted significant attention due to their influence on the preparation and performance of the waterborne polyurethane. Herein, a novel undecylenic‐based primary glycol (UPG) without dangling chains synthesized and the oleic‐based primary glycol (OPG) with dangling chains reported by our previous work were used to prepare straight‐chain and dangling‐chain bio‐based waterborne polyurethane (BWPU), respectively, to study the difference between the two diols and the effects of dangling chains on the synthesis and performance of BWPU. First, the UPG without dangling chains displayed higher activation energy (Ea/Eo = 77.72/80.56 kJ mol−1) and longer reaction end point of prepolymer (240 min), indicating relatively lower reactivity to isocyanate. In addition, the dangling chains were found to influence the dispersion stability of BWPU, and the minimum dosage of DMPA for maintaining dispersion stability was 6.5 wt% for OPG but 5.5 wt% for UPG. The average particle size of BWPU is greater for OPG than for UPG with the same DMPA content. Finally, performance studies revealed that dangling‐chain BWPU showed higher hydrophobicity, extensibility, and low temperature resistance, but lower thermal stability (Td5%) and tensile strength. This work comprehensively clarified the effects of linear and branched bio‐based polyols on the synthesis and properties of BWPU, and provided guidance for the development and application of bio‐based polyols and BWPU coatings.