There are some studies on the synthesis of polyurea microcapsules. However, there is hardly a case where both green solvents and non-toxic isocyanates are used, especially in microfluidics. In this work, an environmentally friendly chemical system of interfacial polymerization (isocyanate: HDB-LV; solvent: octyl salicylate or dibutyl adipate) is tested for the first time to produce polyurea microcapsules. The size of microcapsules is calibrated at 78 μm by microfluidics to quantitatively analyze the relationships among shell thickness, encapsulation efficiency and isocyanate concentrations. The influences of solvent types and reactant concentrations on the shape, morphology and shell thickness of microcapsules are studied. Esters with low water miscibility and low amine concentrations (lower reaction rate) are crucial for the formation of spherical microcapsules. An ester with high water miscibility can diffuse into the continuous phase during encapsulation, which results in broken microcapsules. A high concentration of amine can probably cause cross-linking not only at the interface but also inside the droplet template, which leads to microcapsule deformation. A linear relationship is observed between the shell thickness of microcapsules and the isocyanate concentration. Overall, a high encapsulation efficiency (more than 90%) for octyl salicylate is achieved with polyurea microcapsules.