The on-board flat-panel cone-beam computed tomography (CBCT) lacks molecular/functional information for current online image-guided radiation therapy (IGRT). It might not be adequate for adaptive radiation therapy (ART), particularly for biologically guided tumor delineation and targeting which might be shifted and/or distorted during the course of RT. A linear accelerator (Linac) gantry-mounted on-board imager (OBI) was proposed using a single photon counting detector (PCD) panel to achieve single photon emission computed tomography (SPECT), energy-resolved spectral CT, and conventional CBCT triple on-board imaging, which might facilitate online ART with an addition of volumetric molecular/functional imaging information. Methods: The system was designed and evaluated in the GATE Monte Carlo platform. The OBI system including a kV-beam source and a pixelated cadmium zinc telluride (CZT) detector panel mounted on a medical Linac orthogonally to the MV beam direction was designed to obtain online CBCT, spectral CT, and SPECT tri-modal imaging of patients in the treatment room. The spatial resolutions of the OBI system were determined by imaging simulated phantoms. The CBCT imaging was evaluated by a simulated contrast phantom. A PMMA phantom containing gadolinium was imaged to demonstrate quantitative imaging of spectral-CT/CBCT of the system. The capability of tri-modal imaging of the OBI was demonstrated using three different spectral CT imaging methods to differentiate gadolinium, gold, calcium within simulated PMMA and the SPECT to image radioactive 99m Tc distribution. The dual-isotope SPECT imaging of the system was also evaluated by imaging a phantom containing 99m Tc and 123 I. The radiotherapy-related parameters of iodine contrast fraction and virtual non-contrast (VNC) tissue electron density in the Kidney1 inserts of a simulated phantom were decomposed using the Bayesian eigentissue decomposition method for contrastenhanced CBCT/spectral-CT of the OBI in a single scan. Results: The spatial resolutions of CBCT and SPECT of the OBI were determined to be 15.1 lp/cm at 10% MTF and 4.8-12 mm for radii of rotation of 10-40 cm, respectively. In CBCT image of the contrast phantom, most of the soft-tissue inserts were visible with sufficient spatial structure details. As compared to the CBCT image of gadolinium, the spectral CT image provided higher image contrasts. Calcium, gadolinium, and gold were separated well by using the spectral CT material imaging methods. The reconstructed distribution of 99m Tc agreed with the spatial position within the phantom. The two isotopes were separated from each other in dual-isotope SPECT imaging of the OBI. The iodine fractions and the VNC electron densities were estimated in the iodine-enhanced Kidney1 tissue inserts with reasonable RMS errors. The main procedures of the tri-modal imaging guided online ART workflow were presented with new functional features included. Conclusions: Using a single photon counting CZT detector panel, an on-board SPECT, spectral CT, and CBCT tr...