Hybrid waveguides consisting of two-dimensional layered materials pad on the surface of optical waveguides suffer from a nonuniform and loose contact between the two-dimensional material and the waveguide, which can reduce the efficiency of the pulsed laser. Here, we present high-performance passively Q-switched pulsed lasers in three distinct structures of monolayer graphene-Nd:YAG hybrid waveguides irradiated by energetic ions. The ion irradiation enables the monolayer graphene a tight contact and strong coupling with the waveguide. As a result, Q-switched pulsed lasers with narrow pulse width and high repetition rate are obtained in three designed hybrid waveguides. The narrowest pulse width is 43.6 ns, provided by the ion-irradiated Y-branch hybrid waveguide. This study paves the way toward developing on-chip laser sources based on hybrid waveguides by using ion irradiation.