The development of facile techniques for precisely patterning complex metal and metal oxide nanostructures is essential for catalytic nanosystems and optical and electronic nanodevices. Herein, we report a general strategy for designing and fabricating metal and metal oxide nanoclusters (MMONs) with arbitrarily prescribed patterns on DNA origami templates. The valuable feature of our approach lies in the site-specific arrangement of thiol groups on DNA origami, which act as reaction centers, initiating in situ MMONs growth. This strategy can be generalized to the patterning of arbitrary geometries and various inorganic materials, which will aid the generation of complex and precisely arranged components for customized functional nanoarchitectures.