Silicon (Si) is a promising material for lithium ion battery (LIB) anodes due to its high specific capacity. To overcome its shortcomings such as insulation property and large volume change during the charge–discharge process, a novel hybrid system, Si nanoparticles encapsulated in hollow graphitized carbon nanofibers, is studied. First, electrospun polyacrylonitrile (PAN)–Si hybrid nanofibers were obtained using water as the collector. The loose nanofiber lumps suspended in water have large inter-fiber distance, allowing in situ coating of a thin layer of polydopamine (PDA), the source for graphitized carbon, uniformly throughout the system. The designed morphology and structure were then realized by etching and calcination, and the morphology and structure were subsequently verified by various analytical techniques. Electrochemical measurements show that the resulting hollow hybrid nanofibers (C-PDA–Si NFs) exhibit much better cycling stability and rate capacity than conventional C/Si nanofibers derived by electrospinning of PAN–Si followed by calcination. For instance, the capacity of C-PDA–Si NFs is as high as 72.6% of the theoretical capacity after 50 cycles, and a high capacity of 500 mA h g⁻¹ can be delivered at a current density of 5 A g⁻¹. The significantly improved electrochemical properties of C-PDA–Si NFs are due to the excellent electrical conductivity of the carbonized PDA (C-PDA) shell that compensates for the insulation property of Si, the high electrochemical activity of C-PDA, which has a layered structure and is N-doped, the hollow nature of the nanofibers and small size of Si nanoparticles that ensure smooth insertion–extraction of lithium ions and more complete alloying with them, as well as the buffering effect of the remaining PAN-derived carbon around the Si nanoparticles, which stabilizes the structure.