Utilizing renewable sources of energy to produce hydrogen by electrocatalytic water splitting has emerged as an achievable answer to the issues associated with fossil fuels. Designing an efficient electrocatalyst for hydrogen evolution reaction (HER) is an important research area and it is essential to develop the catalyst that is electrocatalytically active, stable and economical to overcome the use of high-cost Pt for HER reaction. In this regard, we have synthesized a novel graphitic carbon nitride-based Schiff base modified silane linked palladium (II) nanocatalyst (g-C3N4-Scb@Pd). The g-C3N4-Scb@Pd evaluated for electrocatalytic hydrogen evolution reaction showed excellent catalytic activity exhibiting lowest overpotential of 40.3 mV at 10 mA/cm2 compared to its other counterparts such as g-C3N4-Pd and g-C3N4. The enhanced activity of g-C3N4-Scb@Pd can be ascribed to higher tendency for charge transfer contributed by Schiff base modified silane bonding between Pd and g-C3N4 forming efficient pathway for improved electron migration in addition to synergistic effect of Pd and g-C3N4. Further, the DFT analysis identifies the active sites, electronic structures and analyses the underlying phenomena to elucidate the possible reason for improving the HER performance from g-C3N4 towards Pd@g-C3N4. This work introduces a new approach for designing and engineering the g-C3N4 based efficient electrocatalysts.