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Hydrogen evolution reaction (HER) takes place immediately after the reduction of Co nanoparticles (NPs) and varies the structure of the Co NPs. The Co NPs deposited by low cathodic current exhibit their hcp- 〈1011〉 parallels the surface normal. To increase the cathodic current can increase the ratio of the polar magnetization to the longitudinal one. This is referred to an increasing population density of the Co NPs which have hcp(0002) structure during the very early depositing stage. However, for further deposition, the intensive HER in such a high cathodic current could vary the shape of the Co nanoparticles. In order to make the Co NPs to persist their hcp(0002) structure, a double pulse current technique was chosen. The population density of the Co NPs is significantly controlled by the first high current pulse and the ratio is obviously increased. This implies that the HER effect plays an important role in the initial nucleation structure of the Co NPs. This provides us a method to control the structure and magnetism of the Co NPs by choosing a suitable combination of current pulses.