As one class of important functional materials, transition metal phosphides (TMPs) nanostructures show promising applications in catalysis and energy storage fields. Although great progress has been achieved, phase‐controlled synthesis of cobalt phosphides nanocrystals or related nanohybrids remains a challenge, and their use in overall water splitting (OWS) is not systematically studied. Herein, three kinds of cobalt phosphides nanocrystals encapsulated by P‐doped carbon (PC) and married with P‐doped graphene (PG) nanohybrids, including CoP@PC/PG, CoP‐Co2P@PC/PG, and Co2P@PC/PG, are obtained through controllable thermal conversion of presynthesized supramolecular gels that contain cobalt salt, phytic acid, and graphene oxides at proper temperature under Ar/H2 atmosphere. Among them, the mixed‐phase CoP‐Co2P@PC/PG nanohybrids manifest high electrocatalytic activity toward both hydrogen and oxygen evolution in alkaline media. Remarkably, using them as bifunctional catalysts, the fabricated CoP‐Co2P@PC/PG|| CoP‐Co2P@PC/PG electrolyzer only needs a cell voltage of 1.567 V for driving OWS to reach the current density at 10 mA cm−2, superior to their pure‐phase counterparts and recently reported bifunctional catalysts based devices. Also, such a CoP‐Co2P@PC/PG|| CoP‐Co2P@PC/PG device exhibits outstanding stability for OWS. This work may shed some light on optimizing TMPs nanostructures based on phase engineering, and promote their applications in OWS or other renewable energy options.