Crystallization is a universal phenomenon underpinning many industrial and natural processes and is fundamental to chemistry and materials science. However, microscopic crystallization pathways of nanoparticle superlattices have been seldom studied mainly owing to the difficulty of real-time observation of individual self-assembling nanoparticles in solution. Here, using in situ electron microscopy, we directly image the full self-assembly pathway from dispersed nanoparticles into ordered superlattices in nonaqueous solution. We show that electron-beam irradiation controls nanoparticle mobility, and the solvent composition largely dictates interparticle interactions and assembly behaviors. We uncover a multistep crystallization pathway consisting of four distinct stages through multi-order-parameter analysis and visualize the formation, migration, and annihilation of multiple types of defects in nanoparticle superlattices. These findings open the door for achieving independent control over imaging conditions and nanoparticle assembly conditions and will enable further study of the microscopic kinetics of assembly and phase transition in nanocolloidal systems.