The medical linear accelerator (linac) integrated with a kilovoltage (kV) flat-panel imager has been emerging as an important piece of equipment for image-guided radiation therapy. Due to the sagging of the linac head and the flexing of the robotic arms that mount the x-ray tube and flat-panel detector, geometric nonidealities generally exist in the imaging geometry no matter whether it is for the two-dimensional projection image or three-dimensional cone-beam computed tomography. Normally, the geometric parameters are established during the commissioning and incorporated in correction software in respective image formation or reconstruction. A prudent use of an on-board imaging system necessitates a routine surveillance of the geometric accuracy of the system like the position of the x-ray source, imager position and orientation, isocenter, rotation trajectory, and source-to-imager distance. Here we describe a purposely built phantom and a data analysis software for monitoring these important parameters of the system in an efficient and automated way. The developed tool works equally well for the megavoltage (MV) electronic portal imaging device and hence allows us to measure the coincidence of the isocenters of the MV and kV beams of the linac. This QA tool can detect an angular uncertainty of 0.1 degrees of the x-ray source. For spatial uncertainties, such as the source position, the imager position, or the kV/MV isocenter misalignment, the demonstrated accuracy of this tool was better than 1.6 mm. The developed tool provides us with a simple, robust, and objective way to probe and monitor the geometric status of an imaging system in a fully automatic process and facilitate routine QA workflow in a clinic.