Abstract: The results of 12-year located fertilization in grey desert soil of Xinjiang showed that treatments of N, NP, NK, NPK could improve the grain quality in some indexes compared with CK. The contents of crude protein, essential and total amino acid, characters of the flour and dough qualities of long-term without N application (PK) declined significantly, and the ash content increased. Compared with chemical fertilizer applying only (N, NP, NK, PK, NPK) and CK, treatment of NPK with farm yard manure (NPK+M) had a better effect on improving flour and dough qualities in most of indexes. Contrast to CK, the treatment of crop straw return to field (NPK+S) increased the 1000-seed weight and dough tenacity ability and decreased the other characters in a certain degree. Chemical fertilizer combined with farm yard manure was very important to build up soil fertility, increase yield and improve grain quality.