Long-range ordered nanostructures are prepared in the poly(styrene)-block-poly(ε-caprolactone) diblock copolymer thin films using micromolding. We evaluated the change in crystallinity based on grazing-incidence X-ray diffraction and proved that the crystallinity increased with the decrease of the mold size. This means that ordered nanostructures with atomic length scale order can be adjusted by tuning the mesoscale confinement. The inherent mechanism was the cooperation of geometric confinement, microphase structure and surface-induced ordering of PS-b-PCL in the melt, which paved the way for the subsequent crystal growth. These findings establish a route to promote the cost-effective nanofabrication by combining the mature microfabrication technique with the emerging directed self-assembly of block copolymers.