At present, it is still a challenge to prepare multifunctional composite nanomaterials with simple composition and favorable structure. Here, multifunctional Fe3O4@nitrogen-doped carbon (N-C) nanocomposites with hollow porous core-shell structure and significant electrochemical, adsorption and sensing performances were successfully synthesized through the hydrothermal method, polymer coating, then thermal annealing process in nitrogen (N2) and lastly etching in hydrochloric acid (HCl). The morphologies and properties of the as-obtained Fe3O4@N-C nanocomposites were markedly affected by the etching time of HCl. When the Fe3O4@N-C nanocomposites after etching for 30 min (Fe3O4@N-C-3) were applied as the anodes for lithium-ion batteries (LIBs), the invertible capacity could reach 1772 mA h g−1after 100 cycles at the current density of 0.2 A g−1, which is much better than that of Fe3O4@N-C nanocomposites etched, respectively, for 15 min and 45 min (948 mA h g−1and 1127 mA h g−1). Additionally, the hollow porous Fe3O4@N-C-3 nanocomposites also exhibited superior rate capacity (950 mA h g−1at 0.6 A g−1). The excellent electrochemical properties of Fe3O4@N-C nanocomposites are attributed to their distinctive hollow porous core-shell structure and appropriate N-doped carbon coating, which could provide high-efficiency transmission channels for ions/electrons, improve the structural stability and accommodate the volume variation in the repeated Li insertion/extraction procedure. In addition, the Fe3O4@N-C nanocomposites etched by HCl for different lengths of time, especially Fe3O4@N-C-3 nanocomposites, also show good performance as adsorbents for the removal of the organic dye (methyl orange, MO) and surface-enhanced Raman scattering (SERS) substrates for the determination of a pesticide (thiram). This work provides reference for the design and preparation of multifunctional materials with peculiar pore structure and uncomplicated composition.