The common wheat variety Chinese Spring (CS) chromosome substitution line CS-1S^l(1B) was used in this study, in which the 1B chromosome in CS (Triticum aestivum L., 2n = 6x = 42, AABBDD) was substituted by the 1S^l from Aegilops longissima (2n = 2x = 14, S^lS^l). The results showed that the substitution of 1B in CS by 1S^l chromosome could significantly increase amylopectin and total starch contents. The dynamic changes in starch granules during grain development in CS and CS-1S^l(1B) demonstrated that the substitution line possessed higher amount of A-type starch granules and greater diameter of both A- and B-granules. qRT-PCR revealed that some key genes involved in starch biosynthesis, such as starch synthases (SSI, SSII and SSIII), starch branching enzymes (SBE IIa and SBE IIb) and granule-bound starch synthase (GBSS I), displayed higher transcript levels of mRNA expressions during grain development in CS-1S^l(1B). Our results indicate that the substituted 1S^l chromosome carries important genes that influence starch granule development and starch biosynthesis, which may be used as potential gene resources for improvement of wheat starch quality.