Energy storage devices have become vital parts of our routine life. Among the numerous candidates, lithium ion batteries are considered the most favorable energy storage systems. MoSe2 consists of Se-Mo-Se atom layers bounded with van-der Waals forces and is highly favored for lithium ion intercalation and extraction. This paper establishes a simple and economical one-pot chemical method to synthesize MoSe2 nanostructures for lithium ion battery anode material. Raman scattering confirmed the 1T@2H MoSe2 mixed phase structure, transmission electron microscopy showed 2H and 1T phase contours in the MoSe2 nanosheet, and scanning electron microscopy showed the nanograin honeycomb structured morphology. The 1T@2H MoSe2 nanostructures deliver enhanced primary discharge capacity 843 mAh/g at 100 mA/g with 99% Coulombic efficiency after 100 cycles. Electrochemical results confirmed the 1T@2H MoSe2 nanostructure would be an excellent anode material and a promising candidate for high performance lithium ion batteries.