Recent research has demonstrated that the Macroscopic Fundamental Diagram (MFD) is reliable and practical tool for modeling traffic dynamics and network performance in single-mode (cars only) urban road networks. In this paper, we first extend the modeling of the single-mode MFD to a bi-modal (bus and cars) one. Based on simulated data, we develop a three-dimensional MFD (3D-MFD) relating the accumulation of cars and buses, and the total circulating flow in the network. We propose an exponential function to capture the shape of the 3D-MFD, which shows a good fit to the data. We also propose an elegant estimation for passenger car equivalent of buses (PCU), which has a physical meaning and depends on the bi-modal traffic in the network. Moreover, we analyze a 3D-MFD for passenger network flows and derive its analytical function. Finally, we investigate an MFD for networks with dedicated bus lanes and the relationship between the shape of the MFD and the operational characteristics of buses. The output of this paper is an extended 3D-MFD model that can be used to (i) monitor traffic performance and, (ii) develop various traffic management strategies in bi-modal urban road networks, such as redistribution of urban space among different modes, perimeter control, and bus priority strategies.