Through the different functionalities on Au nanosphere (AuNSs) and Au nanorod (AuNRs) surfaces, we successfully control AuNSs attachment onto either the end or side surface of anisotropic AuNRs via bio-recognition, and then consciously construct side-by-side or end-to-end assembly nanostructures. This study provides a feasible approach to organize nanoparticles with different morphologies into controllable assembly geometries, which can potentially benefit the construction of future nanodevices. ; National Natural Science Foundation of China [90923042, 21101130, 30970733, 81171448]; National Basic Research Program of China (973 Program) [2010CB732402]; Specialized Research Fund for the Doctoral Program of Higher Education [20100121120038]; Natural Science Foundation of Fujian Province of China [2010J01046]; Fundamental Research Funds for the Central Universities [2010121023]; key laboratory of Biomedical Material of Tianjin