Alloy-/conversion-type metal oxides usually exhibit high theoretical lithium storage capacities but suffer from the large volume change induced electrode pulverization and the poor electric conductivity, which limit their practical applications. Hybrid/mixed metal oxides with different working mechanisms/potentials can display advantageous synergistic enhancement effect if delicate structure engineering is performed. Herein, atomically hybridized SnO/CoO nanocomposites with amorphous nature are successfully cast onto the porous N-doped carbon (denoted as NC) nanoflakes through facile pyrolysis of the tin (II) 2-ethylhexanoate (CHOSn) and cobalt (II) 2-ethylhexanoate (CHOCo) mixture within NC nanoflakes in air at 300 °C for 1 h. The Sn/Co atomic ratio and the loading amount of SnO/CoO can be readily controlled, whose effect on lithium storage are investigated as anodes for lithium ion batteries (LIBs). Notably, SnO/CoO@NC (R = 1.25) nanoflakes exhibit the most excellent lithium storage properties, delivering a reversible capacity of 1450.3 mA h g after 300 cycles at 200 mA g, which is much higher than that of the single metal oxide SnO@NC and CoO@NC electrodes.