Hyperentanglement, the entangled states in the multiple degrees of freedom (DOFs) of a photon system simultaneously, has attracted much attention recently as it can increase the capacity of quantum communication largely. Here we present the first scheme for concentrating the nonlocal two-photon six-qubit systems entangled in polarization, spatial-mode, and time-bin DOFs with linear optics. We construct the parity-check gates for the quantum states of nonlocal photon systems in all the three DOFs with linear-optical elements. Fortunately, our parity-check gate for one DOF does not affect the quantum states in the other two DOFs, which makes our hyperentanglement concentration protocol (hyper-ECP) can be implemented conveniently for polarization–spatial–time-bin partially hyperentangled states. This hyper-ECP is practical as it requires only linear-optical elements, and it can be directly generalized to improve the entanglement of nonlocal multi-photon systems entangled in three DOFs in the long-distance high-capacity quantum communication.