Embodiments of the invention provide a step length estimation method, a pedometer and a step counting system. According to the present invention, when step counting is started, based on each preset duration, according to the human body motion acceleration detected by an acceleration sensor within the preset duration, the motion indexes of the human body within the preset duration are determined, wherein the motion indexes comprise motion step frequency and/or motion intensity; based on the numerical relationship between the pre-statistical motion indexes and the human body step length/height ratio, and the motion indexes, the step length/height ratio is determined; and according to the human body height, the motion step length within the preset duration is estimated; and with the step length estimation method, the pedometer and the step counting system, the problem that the calculation is not accurate when the pedometer uses the step length output by the user to calculate the motion distance is solved in the prior art. The present invention relates to the technical field of computers.