Herein, cobalt ammine complexes are combined with alkali-resistant polyoxoniobates (PONbs) at the molecular level to obtain two new organic-inorganic hybrid Co-containing PONbs with the same polyanions but different Co contents. The Co-containing PONb with higher Co content exhibits superior hydrogen evolution reaction (HER) activity under highly alkaline conditions, which is better than the results for the similar Cu-containing PONb, highlighting the critical role of cobalt in improving HER performance. This study provides a new insight into the relationship between the structural properties of metal complexes during electrocatalysis.