In this work, the thermoelectric generator (TEG) layer has been combined with conventional layers of photovoltaic-thermal (PVT) modules to use the waste heat and increase the efficiency. To reduce the cell temperature, there exists a cooling duct in the bottom of the PVT-TEG unit. Type of fluid within the duct and structure of duct can change the performance of the system. So, hybrid nanofluid (mixture of Fe3O4and MWCNT with water) has been replaced instead of pure water and three various configurations of cross section [STR1 (circular), STR2 (rhombus), STR3 (elliptic)] have been implemented. Through the tube incompressible laminar flow of hybrid nanofluid has been solved while in solid layers of panel, pure conduction equation has been simulated involving heat sources resulting from optical analysis. According to simulations, the third structure (elliptic) has the best performance and rise of inlet velocity causes overall performance to enhance about 6.29%. The values of thermal and electrical performances for elliptic design with equal fractions of nanoparticles are 14.56% and 55.42%, respectively. With the best design, electrical efficiency improves about 16.2% in comparison with an uncooled system.