Hydrogen (H2) generation from natural biological metabolic products has remained a huge challenge for the energy arena. However, designing a catalytic system with complementary properties including high surface area, high loading, and easy separation offers a promising route for efficient utilization of nanoreactors for prospective H2 suppliers to a fuel cell. Herein, selective dehydrogenation of formic acid (FA) as a natural biological metabolic product to H2 and CO2 gas mixtures has been studied by supporting ultrafine palladium nanoparticles on organosulfur-functionalized SBA-15 nanoreactor under ultrasonic irradiation. The effects of the porous structure as a nanoreactor, and organosulfur groups, which presented around the Pd due to their prominent roles in anchoring and stabilizing of Pd NPs, studied as a superior catalyst for selective dehydrogenation of FA. Whole catalytic systems were utilized in ultrasonic irradiation in the absence of additives to provide excellent TOF/TON values. It was found that propose catalyst is a greener, recyclable, and more suitable option for the large-scale application and provide some new insights into stabilization of ultra-fine metal nanoparticle for a variety of applications.