The shape, size and packing structure of the hydration products in the plain and fly ash (FA) cement pastes were conducted by the atomic force microscope (AFM). The water-binder ratio was 0.35, two cement pastes was plain cement as control and FA replacing 30% cement by mass, and the curing ages were adopted the 7 days and 90 days respectively. The results show that there are many round particles about 80nm. However, the size of the round particles has been tended to become smaller with the curing time increase. But the packing structure became tight because of the rearranged particle with the curing time increase. Moreover, fly ash would affect markedly the shape, size and packing structure of hydration products. The results indicate that C-S-H clusters in FA cement paste appear the flat shape and looser packing structure due to its low calcium and silicate ratio.