In this review paper, we introduce representative research work on single atomic/molecular manipulations by atomic force microscopy (AFM), which possesses extraordinary ability to resolve atomic and chemical bonds, and charge density distributions of samples. We first introduce the working principle of AFM, then focus on recent advances in atom manipulation at room temperature, force characterization in the process of atom/molecule manipulation, and charge manipulation on insulating substrates. This review covers the following four aspects: 1) the imaging principle of AFM and the atomic characterization of typical molecules such as pentacene and C ₆₀; 2) the mechanical manipulation and atomic recognition capability of AFM at room temperature; 3) the characterization of forces in the process of surface isomerization and adsorption configuration changes of the molecules; 4) the manipulation of charge states and the characterization of single and multiple molecules on insulating substrates. The capability of manipulation by AFM in these fields widens the range in atomic/molecular manipulation, which can provide new and well-established schemes for the analysis and precise control of the manipulation process, and can further contribute to the construction of nanoscale devices, such as “molecular switches” and storage components.