Transition metal phosphides (TMPs) have recently emerged as prominent energy conversion and storage materials owing to their unique physicochemical property. Nevertheless, it’s still a difficult task to obtain phase-control of TMPs owing to multiple energetically favorable stoichiometries. Herein, a phase-controllable cobalt phosphide@C with the pomegranate core–shell structure are successfully realized by employing Co-glycerate as precursors and phytic acid (PA) as P sources, etching and coordination agents. With the presence of six phosphoryl groups and the strong coordination ability, PA allows the self-phosphating of Co atoms and the P-doped carbon shell, as well as the confinement of the obtained nanoparticles Additionally, as an organic acid, PA can etch the Co-glycerate precursors with the formation of hollow structures. With different etching time, metal-rich phosphides Co2P@C and monophosphides CoP@C are successfully achieved. When applied as anode materials, CoP@C demonstrates superior lithium storage performance by delivering a prominent reversible capacity up to 1187 mAh/g at 0.1 A/g and shows no capacity loss at 1 A/g after 500 cycles. This work presents a simple protocol to obtain TMPs with tunable metal/phosphorus ratios, phase selectivity and interface engineering, which could be applied in the field of energy storage and electrocatalysis.