The key prerequisite for fully rationalizing and optimizing thermoelectric performance of molecular devices is to effectively overcome the inherent mismatch between electrode molecular orbital energy and Fermi level (FL). Two structures were formed by stacking bis-phenylethynyl-anthrancene (BPA-molecule) with B-doped armchair/zigzag graphene nanoribbon (AGNR@B/ZGNR@B) electrodes. Optimal distance between the molecule and these two B-doped graphene nanoribbons was related to interfacial stacking mode (BPA-AGNR@B optimization distance is 3.387\\AA for the case of top-site stacking, and it is 3.472\\AA for malposed stacking of BPA-ZGNR@B). Thermal conductivities of both the two B-doped systems based on mass mismatch mechanism are greatly improved at FL. The role of mass matching effect on total thermal conductance of BPA-AGNR@B system is pivotal to result in significant enhancements, but it is not the case for BPA-ZGNR@B, because large layer spacing weakens mass matching effect. In addition, boron-doped molecular junctions (BPA-AGNR@B and BPA-ZGNR@B) show an excellent thermoelectric quality factor (ZT) of 3.5/3.3 near FL.