A strategy for the preparation of metal oxide-carbon composite powders with yolk-shell structure by simple spray pyrolysis is introduced. Mn–Sn–O–C composite powders with yolk-shell structure representing the first target material are prepared by one-pot spray pyrolysis and their formation mechanism is evaluated. Phase separation of polyvinylpyrrolidone (PVP), Sn, and Mn components during the drying stage of droplets plays a key role in the formation of yolk-shell structured composite powders. The repeated combustion and contraction processes of the dried powders under N2 atmosphere produce the desired Mn–Sn–O–C composite powders with yolk-shell structure. The shell and core parts of the yolk-shell powders prepared directly by spray pyrolysis at 900 °C are MnO–Mn2SnO4–C and Sn–Mn2SnO4–C composites, respectively. The initial discharge capacities of the composite powders prepared at 700 and 900 °C at the current density of 1 A g−1 are 1058 and 1204 mA h g−1, respectively. The discharge capacities of the composite powders prepared at 900 °C for the 2nd and 100th cycle are 803 and 784 mA h g−1, respectively. The structural stability of the Mn–Sn–O–C composite powders with yolk-shell structure during cycling results in good electrochemical performance.