Hydrogen peroxide (H2O2), as a clean and green oxidant, is widely used in many fields. The direct synthesis of H2O2 (DSHP) from H2 and O2 has attracted most research interest because it relates to a facile, environmentally friendly, and economic process. Yolk–shell Pd-M@HCS (hollow carbon sphere) (M = Co, Ni, Cu) nanocatalysts, in which the bimetal nanoparticle is the core and porous carbon works as the shell layer, are reported in this work. It was found that catalytic activities were enhanced because of the introduced M metals. Additionally, the different mass ratios of Pd to Co (mPd/mCo) were further investigated to improve the catalytic performance for the DSHP. When mPd/mCo was 4.4, the prepared Pd-Co@HCS-(4.4) catalyst, with an average Pd nanoparticle size of 7.30 nm, provided the highest H2O2 selectivity of 87% and H2O2 productivity of 1996 mmolgPd−1·h−1, which were increased by 24% and 253%, respectively, compared to Pd@HCS.