The bipolar fatigue behavior of (K,Na)NbO3 (KNN)-based lead-free piezoceramics was investigated. A comparative analysis demonstrated that CaZrO3-modified KNN ceramics exhibited highly enhanced bipolar fatigue resistance due to the reduced lattice distortion (c/a ratio) and coexistence of orthorhombic and tetragonal phases. The hypothesis was verified by systematical studies of cycle-dependent large and small signal parameters and micro-morphologies. It was identified that mechanical stress induced microstructure damage beneath the electrodes renders the KNN ceramics to be vulnerable to bipolar cycling; while the mild fatigue behavior for CaZrO3-modified ones mainly originates from a thermally reversible domain wall pinning.