Periodically nanopatterned Si structures have been prepared by using a nanosphere lithography technique. The formed nanopatterned structures exhibit good anti-reflection and enhanced optical absorption characteristics. The mean surface reflectance weighted by AM1.5 solar spectrum (300–1200 nm) is as low as 5%. By depositing Si quantum dot/SiO2 multilayers (MLs) on the nanopatterned Si substrate, the optical absorption is higher than 90%, which is significantly improved compared with the same multilayers deposited on flat Si substrate. Furthermore, the prototype n-Si/Si quantum dot/SiO2 MLs/p-Si heterojunction solar cells has been fabricated, and it is found that the external quantum efficiency is obviously enhanced for nanopatterned cell in a wide spectral range compared with the flat cell. The corresponding short-circuit current density is increased from 25.5 mA cm−2 for flat cell to 29.0 mA cm−2 for nano-patterned one. The improvement of cell performance can be attributed both to the reduced light loss and the down-shifting effect of Si quantum dots/SiO2 MLs by forming periodically nanopatterned structures.