In this study, CoNi2S4 microstructures (CoNi2S4 MSs) with urchin-like and flower-like shapes were synthesized by a sacrificial template method based on the Kirkendall effect. The as-prepared CoNi2S4 MSs were used, for the first time, to catalyze the hydrogenation of p-nitrophenol (PNP) by NaBH4. A comparison experiment revealed that the flower-like CoNi2S4 MSs showed better catalytic activity for hydrogenation of PNP than the urchin-like CoNi2S4 MSs at room temperature. The improved catalytic activity of the CoNi2S4 MSs can be attributed to their unique structures under nearly the same sizes.