In this paper, a real-time pipeline centroid calculating structure based on programmable logic devices is designed for Hartmann wavefront sensor with horizontal multi-channel pixel output. The structure is composed of multiplier groups, accumulation cells and dividers. The cells are designed according to the number of output channels and the output pixels’sequence. The centroid calculation latency in one frame is only the calculation time needed for the pixels output at the last pixel clock. In the simulation, when output channels’number is 8 and pixels output at 80MHz clock, centroid calculation latency is less than 0.5μs.