Manipulating the connectivity of external electrodes to central rings of carbon-based molecules in single molecule junctions is an effective route to tune their thermoelectrical properties. Here we investigate the connectivity dependence of the thermoelectric properties of a series of thiophene-diketopyrrolopyrrole (DPP) derivative molecules using density functional theory and tight-binding modeling, combined with quantum transport theory. We find a significant dependence of electrical conductance on the connectivity of the two thiophene rings attached to the DPP core. Interestingly, for connectivities corresponding to constructive quantum interference (CQI), different isomers obtained by rotating the thiophene rings possess the same electrical conductance while those corresponding to destructive quantum interference (DQI) show huge conductance variations upon ring rotation. Furthermore, we find that DQI connectivity leads to enhanced Seebeck coefficients, which can reach 500–700 μV/K. After including the contribution to the thermal conductance from phonons, the full figure of merit (ZT) for the CQI molecules could reach 1.5 at room temperature and it would further increase to 2 when temperature elevates to 400 K. Finally, we demonstrate that doping with tetracyanoquinodimethane can change the sign of the Seebeck coefficients by forming a charge-transfer system with the DPP.