The interplay between Cooper pairs and Bogoliubov‐de Gennes (BdG) quasiparticles is a topic of considerable interest in the quantum properties of solids, but its important ingredient, the sufficient amount of low‐energy quasiparticles to interact with Cooper pairs remains elusive in conventional superconductors. Here a gapless superconductor with coupled paramagnetic atomic layers is used to generate a significant amount of zero‐energy quasiparticles that Anderson‐localize and bifurcate into regions of high and low zero‐energy quasiparticle density of states. The enriched zero‐energy quasiparticles induce puddled superconductivity and Josephson vortices. This discovery not only advances the understanding of the mutual interaction of Cooper pairs and BdG quasiparticles but also opens a new avenue for exploring and controlling exotic quantum phenomena where superconductivity, disorder, and spin degrees of freedom are entangled.