In this work, NH₄F was used as a vital additive to control the morphology of Co₃O₄ precursors on Ni foam in a conventional hydrothermal reaction, and then, via thermal decomposition, to obtain Co₃O₄ material. The amount of NH₄F plays a pivotal role in the formed morphology of the Co₃O₄ precursors, and four morphologies of Co₃O₄ were obtained through close control of the amount of additive: nanowires, thin nanowire-clusters, thick nanowire-clusters, and fan-like bulks. The morphological evolution process of the Co₃O₄ precursors has been investigated according to their intermediates at different reaction stages, and some novel growth mechanisms are proposed: (1) the amount of NH₄F in the solution system affects the chemical composition of the precursors; (2) with an increasing amount of NH₄F in the solution system, the morphology will tend to form more ordered states and more distinct hierarchical structures; (3) with an increasing amount of NH₄F in the solution system, the growth of products will tend to form denser structures; (4) the amount of NH₄F in the solution system will affect the mass loading of products. The four different morphologies of Co₃O₄ were tested as free-standing electrode materials for supercapacitor application. Co₃O₄ with the thin-nanowire-cluster morphology exhibits the best electrochemical performance: the specific area capacitance is 1.92 F cm⁻² at the current density of 5 mA cm⁻² and goes up to 2.88 F cm⁻² after 3000 charge–discharge cycles, while the rate capability is 72.91% at the current density of 30 mA cm⁻².