Sauropsid vertebrates (lepidosaurs, turtles, crocodilians and birds) have evolved a diversity of head shapes and feeding behaviors during their history. A key to understanding this great radiation of reptiles is the physiology of the jaw musculature that powers the feeding apparatus. However, we still know little about jaw muscle mechanics within lineages of reptiles or how this complicated musculoskeletal system has evolved to employ a variety of behaviors. New imaging and computational methods are now enabling an extraordinary view into the 3D anatomy and biomechanics of reptiles and other vertebrates. Here we illustrate several approaches to analyzing jaw muscle morphology and architecture using contrast imaging, 3D fiber tracking, biomechanical analysis, and data visualization methods that offer enormous potential for exploring the anatomy, function and evolution of jaw muscles. We first illustrate basic workflow of 3D jaw muscle imaging, visualization, morphometrics, and interpretation using crocodilian jaw muscle anatomy. Second, we show how homologous jaw muscle bellies evolve among lineages of different reptiles and birds to elicit different functional demands. Third, we show how the 3D architecture of small, deep protractor muscles correlate with different types of cranial kinesis among a sample of lizards and birds. Many of these muscles leave traceable osteological correlates in the fossil record of reptiles and other vertebrates that can better guide inferences of muscle functional anatomy and joint loading environments. These new imaging and analytical approaches offer incredible potential for the quantification of soft tissue morphology and have remarkable applications to comparative biomechanics, ecomorphology, and paleobiology.