In the present work, four types of anionic waterborne polyurethane dispersions (APUD) based on polytetramethylene ether glycol (PTMG) and two aliphatic diisocyanates, dicyclohexylmethane diisocyanate (HMDI) or isophorone diisocyanate (IPDI), were prepared by polymerization methods which for the first time controlled the location (soft or hard segment) of hydroxylated tung oil (HTO) incorporation into the final APUD. The resulting HTO‐containing APUD polymers (HTO‐APUDs) with postpolymerization crosslinking capability were characterized using FTIR, DMA, AFM and water imbibition methods, and compared to model compounds synthesized to have the same parts of chemical structural linkages for band assignment. A common PUD sample, as well as polypropylene oxide (PPG) with molecular weight similar to HTO (Mn = 400), was used to replace it for preparing control samples to highlight the role of long branched chains and conjugated double bonds in HTO. Based on the analysis of multiple H‐bond interactions, the relationship of HTO location in the APUD polymer structure to the soft/hard segment compatibility and the diisocyanate structure was further studied. This work is expected to provide basic data for properties regulation in practical applications by adjusting the chain and phase structure, as well as the intermolecular interactions, in these APUDs.