Given the current shortage of resources and environmental pollution, rationally designing and developing low-cost and high-efficiency bifunctional electrocatalysts is an urgent and challenging task. It is widely recognized that element doping can effectively improve the electrocatalytic activity by adjusting the microstructure, morphology, and electronic structure. Therefore, this work rationally designs and prepares three-dimensional flower-like structured W-doped FeNi2S4/Ni3S2/NF heterojunctions as efficient bifunctional electrocatalysts for overall water splitting. In 1 M KOH, the prepared W-FeNi2S4/Ni3S2/NF electrocatalyst can effectively drive both hydrogen evolution reaction (HER) and oxygen evolution reaction (OER) processes, and only needs overpotentials of 93 and 210 mV to reach current densities of 10 and 50 mA·cm−2. In the double electrode cell composed by W-FeNi2S4/Ni3S2/NF electrocatalyst, a low cell voltage of 1.52 V was required to reach a current density of 10 mA·cm−2, and 91.6% of this value was preserved after 24 h electrolysis operation. The performance of FeNi2S4/Ni3S2/NF electrocatalyst is superior to most of the current bifunctional electrocatalytic materials. Density functional theory (DFT) theoretical calculations also revealed a more intense electron transfer process that can be facilitated by constructing FeNi2S4 and Ni3S2/NF interface, which may be the main reason for the archived excellent electrochemical performance.