Thermally activated redistribution of Si surface atoms is found to be a crucial factor for the growth of aligned Ge dots on pit-patterned Si(001) substrates. A phenomenon of Si accumulation around the edge of pits significantly alters the substrate surface morphology. As the pit spacing is reduced to below 100 nm, a convex morphology developed between adjacent pits causes a chemical potential distribution that drives the Ge dots into the pits. In addition, the pits of an etching depth greater than 60 nm will evolve into truncated inverted pyramids with sharp base corners that provide deep potential wells for the confinement of Ge dots. Perfectly aligned Ge dots are obtained on pit-patterned Si substrates with this range of pit spacing and etching depth. We also find that the initial geometric shape of the pits does not affect the spatial arrangement of Ge dots.