High energy demand has directed the present‐day research towards synthesis and applications of heterostructured nanomaterials such as molybdenum oxysalts over mono‐structured nanomaterials. Molybdenum oxysalt is a promising anode material for lithium ion batteries because of its high theoretical lithium storage capacity (998 mAh g−1) and flexible composition. Engineering the morphology and porosity of a material has proven to be a productive approach towards enhancing its performances. Here in, we have demonstrated a one pot synthesis of mesoporous MnMoO4 nanorods and its enhanced electrochemical performance for Li‐ion battery anode. Several physiochemical techniques have been used to validate the desired properties and purity of the synthesized material. It exhibits high lithiation capacity of 1050 mAh g−1 and stability over 100 cycles at 0.5 C. The enhanced performance is attributed to its structural stability and mesoporous nature.