Cancellation processing is one kind of classical and feasible idea for the purpose of cancelling clutter. A novel method of clutter cancellation for stepped-frequency radar was proposed. Transmitting the basic stepped-frequency waveform, the radar achieves two high resolution range profiles (HRRP) that were produced by the Inverse Discrete Fourier Transform (IDFT) of two frames of return pulses on a same range cell. The two HRRPs which the number of frame interval was chosen rationally were utilized to cancel the clutter, which can keep the HRRP property of a target. To resolve the problems of the clutter shift and the clutter component change induced by the radar platform movement, a strategy was also brought out. The clutter of two HRRPs was aligned by the clutter correlation and then was cancelled. The simulation results validate the correctness of the method.