We present two deterministic schemes for constructing a CNOT gate and a Toffoli gate on photon-atom and photon-atom-atom hybrid quantum systems assisted by bad cavities, respectively. They are achieved by cavity-assisted photon scattering and work in the intermediate coupling region with bad cavities, which relaxes the difficulty of their implementation in experiment. Also, bad cavities are feasible for fast quantum operations and reading out information. Compared with previous works, our schemes do not need any auxiliary qubits and measurements. Moreover, the quantum circuits for these gates are simple, especially that for our Toffoli gate as only a quarter wave packet is used to interact the photon with each of the atoms every time. These atom-cavity systems can be used as the quantum nodes in long-distance quantum communication as their relatively long coherence time is suitable for multi-time operations between the photon and the system. Our calculations show that the average fidelities and efficiencies of our two universal hybrid quantum gates are high with current experimental technology. ; Comment: 10 pages, 4 figures, one column