Increasing demands for pollution-free energy resources have stimulated intense research on the design and fabrication of highly efficient, inexpensive, and stable non-noble earth-abundant metal catalysts with remarkable catalytic activity for the oxygen evolution reaction (OER) and hydrogen evolution reaction (HER). Morphology control of the catalysts is widely implemented as an effective strategy to change the surface atomic coordination and increase the catalytic behavior of the catalysts. In this study, we have designed a series of Mn-Co catalyts with different morphologies on the graphite paper substrate to enhance OER and HER activities in alkaline media. The prepared catalysts with different morphologies were successfully obtained by adjusting the amount of ammonium fluoride (NHF) in the hydrothermal process. The electrochemical tests display that the cubic-like Mn-Co catalyst with pyramids on the faces at a concentration of 0.21 M NHF exhibits the best activity toward both OER and HER. The cubic-like Mn-Co catalyst with pyramids on the faces showed overpotentials of 240 and 82 mV at a current density of 10 mA cm for OER and HER, respectively. Also, the cubic-like Mn-Co catalyst with pyramids on the faces required overpotentials of 319 and 216 mV to reach the current density of 100 mA cm for OER and HER, respectively. The current density of this catalyst at η = 0.32 V was 701.05 mA cm for OER, and for HER, the current density of the catalyst was 422.89 mA cm at η = 0.23 V. The Tafel slopes of the Mn-Co catalyst with cubic-like structures with pyramids on the faces were 78 and 121 mV dec for OER and HER, respectively. A two-electrode overall water electrolysis system using this bifunctional Mn-Co catalyst exhibited low cell voltages of 1.60 in the alkaline electrolyte at the standard current density of 10 mA cm with appropriate stability. These electrochemical merits exhibit the considerable potential of the cubic-like Mn-Co catalyst with pyramids on the faces for bifunctional OER and HER applications.