The effects of the heating conditions and water content on the structure and digestibility of wheat starch (WS)-glycerol monopalmitin (GMP) complexes were investigated. The results showed that the higher water content and the heating conditions of 90°C for 60 min after 100°C for 10 min favor the formation of more WS-GMP complexes with the greater short-range order, although the thermal transition temperatures of GWS-GMP-100 complexes are not significantly affected by the water content. Only the type I complexes were formed under the heating conditions of 90°C for 60 min. The heating conditions of 90°C for 60 min after 100°C for 10 min facilitates the formation of type II complexes, and the amounts of type II complexes increased with increasing water content. The digestion rates of WS-GMP complexes decreased slightly with increasing water content, and the extent of starch amylolysis of WS-GMP complexes significantly decreased after heating further at 90°C compared with that only heating at 100°C. The digestibility of complexes is mainly related to structural order rather than the number of complexes. This study is helpful to further understand starch-lipid complexes by showing that heating conditions and water content influence the formation of WS-GMP complexes.