Majorana fermions feature non-Abelian exchange statistics and promise fascinating applications in topological quantum computation. Recently, second-order topological superconductors (SOTSs) have been proposed to host Majorana fermions as localized quasiparticles with zero excitation energy, pointing out a new avenue to facilitate topological quantum computation. We provide a minimal model for SOTSs and systematically analyze the features of Majorana zero modes with analytical and numerical methods. We further construct the fundamental fusion principles of zero modes stemming from a single or multiple SOTS islands. Finally, we propose concrete schemes in different setups formed by SOTSs, enabling us to exchange and fuse the zero modes for non-Abelian braiding and holonomic quantum gate operations.