Hybrid nanocrystals combining different properties together are important multifunctional materials that underpin further development in catalysis, energy storage, et al., and they are often constructed using heterogeneous seeded growth. Their spatial configuration (shape, composition, and dimension) is primarily determined by the heterogeneous deposition process which depends on the lattice mismatch between deposited material and seed. Precise control of nanocrystals spatial configuration is crucial to applications, but suffers from the limited tunability of lattice mismatch. Here, we demonstrate that surface lattice engineering can be used to break this bottleneck. Surface lattices of various Au nanocrystal seeds are fine-tuned using this strategy regardless of their shape, size, and crystalline structure, creating adjustable lattice mismatch for subsequent growth of other metals; hence, diverse hybrid nanocrystals with fine-tuned spatial configuration can be synthesized. This study may pave a general approach for rationally designing and constructing target nanocrystals including metal, semiconductor, and oxide.