We reported on the dissipative soliton resonance (DSR) phenomenon in a mode-locked Yb-doped fiber laser by using the nonlinear polarization rotation technique. It was found that the multi-pulse oscillation under high pump power could be circumvented by properly adjusting the polarization controllers, namely, the wave-breaking-free rectangular pulse in DSR region was achieved. As the DSR signature, the pulse duration varied from 8.8 ps to 22.92 ns with the increasing pump power. Correspondingly, the maximum pulse energy was 3.24 nJ. The results demonstrated that the DSR phenomenon could exist in Yb-doped fiber lasers, which could be used to achieve wave-breaking-free, ultrahigh-energy pulse.