The field of nanoscience and nanotechnology has achieved significant progress over last thirty years. Complex nanostructures with tunable properties for novel applications have been successfully fabricated and characterized. In this thesis, I will focus on our recent efforts on precise controlled synthesis of zero-dimensional nanostructures as well as fundamental understanding of the physical behavior of as-synthesized nanostructures. Particularly, three topics are presented: (1) Nanoscale crystallinity engineering: we have achieved nanoscale crystallinity control of noble metal nanoparticles with 100% yield by molecular engineering. We have used silver nanoparticles as example to demonstrate synthetic strategy and importance of such control in nanoscale chemical transformation, fundamental electron and phonon couplings and surface plasmon resonance based biological sensors. Such nanoscale crystallinity engineering provides a new pathway for design of complex nanostructures, tailoring nanoscale electronic and mechanical properties as well as controlling classical and quantum coupling interactions; (2) Precise control of core@shell nanostructures: we have developed a new universal strategy denoted as intermediated phase assisted phase exchange and reaction (iPAPER) to achieve layer-by-layer control of shell components in core@shell structures. Tunable plasmonic, optical and magnetic properties of core@shell structures enabled by our iPAPER strategy are further demonstrated. These characterizations are promising for understanding and manipulating nanoscale phenomena as well as assembling nanoscale devices with desirable functionality; and (3) Fundamental spin and structure manipulation of semiconductor quantum dots by hydrostatic pressure. Pressure provides a unique means of modifying materials properties. By measuring dependence of spin dynamics on pressure, we revealed that the spin states of semiconductor quantum dots are very robust. We further provided the first experimental evidence for the existence of a metastable intermediate state before the first-order phase transition of semiconductor quantum dots. Our results are crucial for the future development of quantum information processing based on spin qubits of quantum dots.