The invention relates to a linear water-based polyurethane thickener containing hydrophobic side bases and a preparation method of the linear water-based polyurethane thickener. The preparation method is characterized in that 40 weight percent to 60 weight percent of dibasic alcohol polymers, 10 weight percent to 30 weight percent of diisocyanate and 0 weight percent to 5 weight percent of catalysts are mixed, under the condition of N2 gas existence and the temperature being 50 DEG C to 100 DEG C, the stirring is carried out for 1 to 6 hours, then, 10 weight percent to 30 weight percent of end-capping agents are added, under the condition of the temperature being 50 DEG C to 100 DEG C, the stirring is carried out for 1 to 6 hours, polyurethane prepolymers are prepared, then, 5 weight percent to 20 weight percent of chain extenders are added into the prepared polyurethane prepolymers, the stirring is carried out for 1 to 6 hours under the condition of the temperature being 50 DEG C to 100 DEG C, and the linear water-based polyurethane thickener containing hydrophobic side bases is prepared. The linear water-based polyurethane thickener and the preparation method have the characteristics that no solvent exists, the toxicity is low, the environment is protected, the preparation process is simple, and the like. The prepared linear water-based polyurethane thickener containing hydrophobic side bases is applicable to the thickening of water-based paint, and the obvious thickening effect is realized.