Eugenol-containing oligoorganosilsesquioxanes were synthesized by the method of hydrolytic polycondensation in an active medium under various reaction conditions. The obtained products were characterized by 29Si NMR spectroscopy and MALDI-TOF spectrometry. It was shown that factors such as the reaction temperature, polycondensation duration, and molar ratio between the initial alkoxysilane monomer and acetic acid may affect the molecular weight characteristics and molecular structure of the formed oligomer, like the content of stressed cyclic units (T3, DTT, TDT) and unstressed silsesquioxane units TnDm. In particular, an increase in the ratio of the initial reagents led to an increase in the content of silsesquioxane Tn fragments from 28.2%mol to 41.7%mol, while the number of strained cyclic structures decreased by more than two times. An increase in the synthesis time is of no particular practical value since it was found that the composition of the oligomers synthesized for 6 h and 12 h was practically identical, as was that of the oligomers synthesized for 24 h and 48 h. A noticeable transition in the oligomer composition was observed only when the synthesis time was changed from 12 h to 24 h. Finally, it was shown that the choice of synthesis temperature had the strongest effect on the oligomer composition. The oligomer synthesized at 95 °C contained the highest amount of silsesquioxane Tn fragments, >77%mol, while a Tn fragment content of ~42%mol was observed during the synthesis at 117 °C. It was shown that silsesquioxanes are devitrified at room temperature (Tg from −6.4 to −10.6 °C), and their thermal stability in an inert atmosphere is 300 °C. The synthesized oligomers, due to the presence of hydroxyl-containing eugenol units, may be promising binders and additives for functional epoxy–silicone paints and coating materials.