The noise, caused by tooth to tooth tolerance of flywheel starter ring in momentary crankshaft speed signal, is analyzed and eliminated in this paper. At first the relationship of the noise amplitude with engine speed and engine load are analyzed. Then under the assumption that the noise is independent with the flywheel speed fluctuations, a noise generation model of speed measurement is established. Finally, a new algorithm based on double speed sensors is presented to identify and eliminate the noise. The algorithm is verified by the experiment results to be more efficient than conventional process methods such as filter or static calibration.