The discovery of atomically precise nanoclusters is generally unpredictable, and the rational synthesis of nanoclusters guided by the theoretical design is still in its infancy. Here we present a de novo design of Au36(SR)24 nanoclusters, from theoretical prediction to experimental synthesis and characterization of their physicochemical properties. The crystal structure of an Au36(SR)24 nanocluster perfectly matches the simulated structural pattern with Au4 tetrahedral units along a two-dimensional growth. The Au36(SR)24 nanocluster indeed differs from its structural isomer whose kernel is dissected in an Au4 tetrahedral manner along a one-dimensional growth. The structural isomerism in the Au36(SR)24 nanoclusters further induces distinct differences in ultrafast electron dynamics and chirality. This work will not only promote the atomically precise synthesis of nanoclusters enlightened by theoretical science, but also open up exciting opportunities for underpinning the widespread applications of structural isomers with atomic precision.