In this work, we successfully synthesize ordered Sn/CMK-3 nanocomposites by sonochemical method and carbonization process. XRD results verify that SnO2 has been completely reduced to metal Sn for the samples obtained at 800°C. Sn nanoparticles are good dispersed into the pore channels of ordered CMK-3 for Sn/CMK-3 nanocomposites according to the nitrogen adsorption–desorption isotherms. The lithium storage properties shows that the Sn/CMK-3 nanocomposites obtained at 800°C delivers an initial discharge capacity of 1450mAhg−1, and a reversible capacity as high as 674mAhg−1 after 50 cycles at a current density of 100mAg−1, much higher than those of the samples obtained at 600°C (1352 and 411mAhg−1, respectively). The Sn/CMK-3 nanocomposites obtained at 800°C also demonstrates an excellent rate capability with capacity of 546mAhg−1 even at a current density of 1000mAg−1 after 50 cycles. The improved lithium storage properties of Sn/CMK-3 nanocomposites obtained at 800°C can be attributed to a synergistic reaction between Sn nanoparticles and CMK-3 matrix, as well as the high crystallinity.