ZnO with high theoretical capacity, low cost, natural abundance, and environmentally friendliness is regarded as a promising anode material for lithium-ion batteries (LIBs). Unfortunately, it suffers from low conductivity and huge volume expansion during charge/discharge, which finally leads to rapid capacity degradation and poor rate capability. To overcome these issues, the honeycombed ZnO@N-doped carbon (HC-ZnO@NC) composite with improved performances is prepared in this work. The composite could be easily prepared as an anode for LIBs and sodium-ion batteries (SIBs) by cross-linking and subsequent calcining at a target temperature. When used as an anode for LIBs, it could possess a reversible capacity of 687 mAh g after 500 cycles at a rate of 0.5C. At a higher rate of 2C, 388 mAh g is observed after 500 cycles. Additionally, HC-ZnO@NC also obtains a capacity of 166 mAh g after 200 cycles at 0.5C for SIBs. When the rate reaches 1C, it maintains a capacity of 126 mAh g after 1000 cycles. The outstanding electrochemical metal ion storage properties might be ascribed to the synergistic effect of honeycombed carbon architecture and micro ZnO nanocrystals.