The low scanning speed for atomic force microscopies (AFMs) restricts its further applications, where fast scanning or real-time imaging is required. In some cases (e.g.real-time imaging), repeated scanning tasks on the same area are expected. For this specific application, an on-line scanning time allocation based variable speed scanning method is proposed here to enhance the scanning speed. Specifically, for the repeated scanning tasks, the scanning time for each detected point is intelligently allocated with the information from the aforescanned image and the previous line in the currently-scanned image, according to the sample surface roughness with the consideration of vertical subsystem control dynamics and horizontal positioning accuracy; then for the repeated scanning tasks on the same area, more scanning time can be allocated to the rough area to achieve better imaging performance. This variable speed scanning method can avoid a waste of time on some flat areas, therefore the imaging time can be shortened. The experimental results fully demonstrate the efficacy of this scanning method to enhance the imaging speed and quality.