There is a strong relationship between metazoan body size and extinction risk. However, the size selectivity and underlying mechanisms in foraminifera, a common marine protozoa, remain controversial. Here, we found that foraminifera exhibit size-dependent extinction selectivity, favoring larger groups (>7.4 log10 cubic micrometer) over smaller ones. Foraminifera showed significant size selectivity in the Guadalupian-Lopingian, Permian-Triassic, and Cretaceous-Paleogene extinctions where the proportion of large genera exceeded 50%. Conversely, in extinctions where the proportion of large genera was <45%, foraminifera displayed no selectivity. As most of these extinctions coincided with oceanic anoxic events, we conducted simulations to assess the effects of ocean deoxygenation on foraminifera. Our results indicate that under suboxic conditions, oxygen fails to diffuse into the cell center of large foraminifera. Consequently, we propose a hypothesis to explain size distribution-related selectivity and Lilliput effect in animals relying on diffusion for oxygen during past and future ocean deoxygenation, i.e., oxygen diffusion distance in body.