Electron occupation of orbitals in two-dimensional (2D) layered materials controls the magnitude and anisotropy of the interatomic electron transfer and exerts a key influence on the chemical bonding modes of 2D layered lattices. Therefore, their orbital occupations are believed to be responsible for massive variations of the physical and chemical properties from electrocatalysis and energy storage, to charge density waves, superconductivity, spin-orbit coupling, and valleytronics. Especially in nanoscale structures such as nanoribbons, nanoplates, and nanoflakes, 2D layered materials provide opportunities to exploit new quantum phenomena. In this Account, we report our recent progress in the rational design and chemical, electrochemical, and electrical modulations of the physical and chemical properties of layered nanomaterials via modification of the electron occupation in their electronic structures. Here, we start with the growth and fabrication of a group of layered chalcogenides with varied orbital occupation (from 4d/5d electron configuration to 5p/6p electron configuration). The growth techniques include bottom-up methods, such as vapor-liquid-solid growth and vapor-solid growth, and top-down methods, such as mechanical exfoliation with tape and AFM tip scanning. Next, we demonstrate the experimental strategies for the tuning of the chemical potential (orbital occupation tuned with electron filling) and the resulting modulation of the electronic states of layered materials, such as electric-double-layer gating, electrochemical intercalation, and chemical intercalation with molecule and zerovalence metal species. Since the properties of layered chalcogenides are normally dominated by the specific band structure around which the chemical potential is sitting, their desired electronic states and properties can be modulated in a large range, showing unique phenomena including quantum electronic transport and extraordinary optical transmittance. As the most important part of this Account, we further demonstrate some representative examples for the tuning of catalytic, optical, electronic, and spintronic properties of 2D layered chalcogenides, where one can see not only edge-state induced enhancement of catalysis, quantum Aharonov-Bohm interference of the topological surface states, intercalation modulated extraordinary transmittance, and surface plasmonics but also external gating induced superconductivity and spin-coupled valley photocurrent. Since our findings reflect the critical influences of the electron filling of orbital occupation to the properties in 2D layered chalcogenides, we thus last highlight the importance and the prospective of orbital occupation in 2D layered materials for further exploring potential functionalized applications.