The connection loss which occurs when light transfers from one medium to another attracts additional attention in high-speed and low-power optical links. In this paper, we not only experimentally apply graded index polymer optical waveguide (GI-POW) in the optical link, but also theoretically address some key parameters which largely influence on the connection loss. The experimental setup of this optical link is composed of a VCSEL module, a GI polymer optical waveguide for the transmitter side (WGTx), a GI multimode fiber (GI-MMF), a GI polymer optical waveguide for the receiver side (WGRx), and a detector. We assume that WGTx is launched by a single mode fiber and then measure the connection losses at the interface between any two components. The results show the connection loss between the GI-MMF and the WGRx is approximately 0.4 dB higher than that of the WGTx to the GI-MMF. For the theoretical modeling, we start from the fundamental scalar wave equation, and apply the finite difference beam propagation method (FD-BPM) to simulate the behavior of light inside the waveguide. Furthermore, Fresnel reflection between two media and the scattering effect within polymer optical waveguides are also taken into account. The simulated results show a similar trend to the measured values. Finally, we conclude that the scattering effect could be one of the key issues of GI-POW for maintaining low connection losses with other wave guides and fibers. © 1983-2012 IEEE.