The waxy wheat shows special starch quality due to low amylose content. However, less information is available concerning the physicochemical properties of starch in different waxy wheat under different irrigation. In this study, two wheat near-isogenic lines (NILs) and a normal wheat cultivar were used to investigate the contents, size distribution and crystallinity of starch by biochemical methods, laser-diffraction and X-ray diffraction analysis. The amylose content in wheat grains was the lowest in waxy wheat lines, SJZ8-N, followed by the partly waxy wheat lines, SJZ8-P, and the highest in the normal wheat, SJZ8, with significant differences among wheat lines. Waxy wheat starch had more B-type granules and a higher degree of crystallinity than normal wheat starch, with the order as SJZ8-N > SJZ8-P > SJZ8. When compared with the conventional and water-saving irrigation, the rainfed treatment showed the lowest starch content, amylose content (except SJZ8-N), amylopectin content and relative crystallinity in the three wheat lines indicating that water deficiency was not benefited starch accumulation and crystal formation in wheat grains. It was concluded that (1) wheat lines not only differed in amylose content but also in size distribution and crystallinity of starch; (2) irrigation markedly influenced the physicochemical characteristics of wheat starch; therefore, the irrigation schemes could be adjusted to achieve high-quality wheat production.