Diversification of sexual organs has long attracted evolutionary biologists since it directly results in speciation. Antagonistic co-evolution is often seen in sexual organs of some insects and water birds. We previously found exaggeratedly large penis in long-clawed shrew (Sorex unguiculatus) that reaches nearly half of their head-body length. In this study, we aimed to clarify the pattern, process, and possible mechanisms creating the diversity of shrew’s sexual organs. Taxon sampling and newly developed PCM, called branch specific directional selection analysis, revealed multiple, independent origins of penis elongation in Sorex shrews, although no specific ecological driver was identified. Importantly, vagina size has not been elongated, leading to the rejection of antagonistic co-evolution hypothesis. Sperm competition was also unlikely because testis size did not follow penis size. Video records demonstrated that females court males by twisting hips and tails and that most part of the penis was not inserted to the vagina. Female choice and specific mating behavior might contribute to the penis elongation of some shrews. Behavioral observation of multiple species will shed light on the fascinating patterns of penis diversity.