The young microspore (YM) stage is the most sensitive period for wheat grain formation to abiotic stress. Shading stress during YM stage reduces grain yield mainly due to grain number decrease. However, the photosynthetic base for grain number decrease is still unclear. In this study, 100% (control), 40% (S1), and 10% (S2) of natural light were applied for 1, 3, 5, and 7 days (D1, D3, D5 and D7) during YM stage of two wheat cultivars (Henong825, Kenong9204). The results showed that grain number in Henong825 and Kenong9204 was reduced by - 3.6 to 33.3% and 14.2-72.7%, respectively. The leaf photosynthetic rate (Pn) in Henong825 and Kenong9204 was deducted by 4.5-93.9% and 26.4-99.0%. Under S1-D1, the leaf Pn of Henong825 reducing was mainly due to the reduction of light intensity. With shading intensity and duration increasing, the reasons for leaf Pn decrease were the low light intensity, the low Gs (stomatal conductance) and chlorophyll content, the damage of ultrastructure of chloroplast and photosynthetic system. Under S2-D7, the chlorophyll content, Fv/Fm (maximal photochemical efficiency of photosystem II) and Jmax (maximum electron transport) were reduced by 19.6%, 5.2% and 28.8% in Henong825, and by 29.9%, 7.8% and 33.1% in Kenong9204. After shading removal, the leaf Pn of Kenong9204 under D5 and D7 could not reach to the level of CK. This study indicated that the reduction of leaf Pn was mainly due to the low light intensity under short shading duration (shorter than 3 days), and due to low light intensity and damage of the leaf photosynthetic system under longer shading duration (longer than 5 days), especially for Kenong9204 (shade-sensitive cultivar).