In the process of research on the flow velocity distribution in a partially filled pipe, the under-sampling of measurement data often occurs. For the first time, this problem is solved by the improved non-uniform B-spline curve fitting approximation (NBSC) method. The main innovation of this method is to reconstruct the flow velocity distribution fitting curve with a small amount of non-uniform feature points containing flow velocity information. First, the curvature of a whole discrete sampled data is analyzed, then the weighted threshold is set, and the sampled points that satisfy the threshold are extracted as the initial velocity distribution feature points. Next the node vectors were constructed according to the initial feature points, and the initial interpolation fitting curves are generated. Secondly, by using the relative deviation between the initial approximation curve and each sampled point, new feature points were added where the curve allowable deviation exceeded the specified tolerance, and then a new interpolation fitting curve was obtained. The above procedure was repeated until the fitting curve reached expected accuracy, thus the appropriate feature points were determined. Experimental results showed that, in the case of the same approximation deviation, the proposed NBSC method can solve the problem of under-sampling of measurement data better.