We developed a method for measuring detail channel morphology using a low elevation photographic scanning. This study was conducted in a 36-m step-pool channel segment in a headwater stream of the Ooborasawa monitoring watersheds. A plastic case that equipped with two digital cameras has been installed at a 2.2 m pole ahead. We took photos from 1.8 m above ground surface every 5 seconds and then obtained 3006 photos for 4 hours. Eleven ground control points were installed for measuring relative coordinates of the segment. In addition, we measured the number, height, and length of steps for examining the accuracy of data. Particle size distribution of channel substrate was obtained with 100 random sampling. PhotoScan Professional edition 1.0.0 was used to make a 3 D model, an orthophoto, and a digital surface model. A 5-cm contour was then developed using ArcGIS. Resolution of an obtained topographic model was 0.6 mm per pixel. Because minimum particle size measured by an orthophoto was 1 cm, approximately 88% (greater than 1 cm) of channel substrate was able to be estimated using this method. All of the step structures in the channel were identified. Estimated values of step heights by the topographic model were comparable to the measured values. Our method permits us developing a high-resolution topographical model in a headwater channel, which is important for understanding the dynamics of sediment movement.