Preparing biobased benzoxazine resin through vat photopolymerization 3D printing is of great significance for its sustainable development and application in cutting-edge fields. In this work, biobased guaiacol and eugenol are used as phenol sources, while 2-(2-aminoethoxy) ethanol with flexible ether bonds is used as an amine source to create photoactive benzoxazine monomers, Eu-BzMA and Gu-BzMA. The viscosity of both monomers at room temperature is lower than 150 mPa·s, which can satisfy the requirements of digital light processing (DLP) 3D printing without adding diluents. The thermal and mechanical properties of the 3D printing benzoxazine resins are studied and the relationship between structure and properties is discussed by comparing the two molecules. Eu-BzMA resin has higher thermal decomposition temperature (T5 = 343 °C), higher hardness (0.70 GPa), higher flexural stress (43.5 MPa) and flexural moduli (2.71 GPa); while, Gu-BzMA resin has higher glass transition temperature (176 °C). This is because Eu-BzMA resin shows higher cross-linking density, but contains more flexible structures formed by allyl crosslinking. In this article, a preparation strategy of low viscosity biobased photoactive benzoxazine is proposed and successfully applied to vat photopolymerization 3D printing.