The advancement of cost-effective and efficient electrocatalysts for the hydrogen evolution reaction (HER), oxygen evolution reaction (OER), and oxygen reduction reaction (ORR) is crucial for the progress of clean energy conversion and storage technologies. In this work, cobalt (Co) and cobalt-molybdenum (Mo) bimetallic carbide (Co6Mo6C2) heterostructure grown on carbon nanofibers (denoted as Co-Co6Mo6C2/CNFs) as tri-functional electrocatalyst were prepared by a four-step method. Benefiting from the electronic structure modulation between the heterostructure to improve the catalytic activity, Co-Co6Mo6C2/CNFs exhibits high catalytic activity for HER (91 mV @ 10 mA cm−2), OER (293 mV @ 10 mA cm−2) and ORR (E1/2=0.80 V). Moreover, Co-Co6Mo6C2/CNFs assembled overall water splitting electrolyzer achieves a current density of 10 mA cm−2 with a battery voltage of only 1.70 V and has long-term durability. Zn-air batteries (ZABs) based on Co-Co6Mo6C2/CNFs has a power density of 156.6 mW cm−2 with good stability. This study contributes to the development of inexpensive and efficient transition metal-based multifunctional electrocatalysts.