The preparation of different kinds of nanocomposite materials is a promising approach to alleviate the severe volume changes of Silicon anode materials for lithium-ion secondary batteries. In the present study, a novel nanocomposite Si80Fe16Cr4 was synthesized by high-energy mechanical milling without noticeable contamination. The nano-indentation results revealed that the elastic recoverable energy range of the synthesized nanocomposite is 3.43 times higher than that of Si. The proposed nanocomposite milled for 8 and 10 h recorded a noteworthy reversible capacity of 841 and 812 mAh g−1 even at 100th cycle, with excellent capacity retention. Remarkably, the nanocomposite exhibited a very low initial cycle (1st cycle) capacity loss ∼14%. The crystal separation of the less active silicide phases was determined after the extended cycling, which is advantageous for accommodating the stress produced by the volume changes of the active Si. The primary factors attributed to the excellent electrochemical performance were the size reduction of Si particles to nanometer scale, the formation of the highly elastic matrix, and separation of silicide phases after extended cycling.