Several researchers have investigated the effects of computer simulations on students' learning. However, few have focused on how simulations with authentic contexts influences students' inquiry skills. Therefore, for the purposes of this study, we developed a computer simulation (FossilSim) embedded in an authentic inquiry lesson. FossilSim integrated data from real field investigations with geological laws for identifying the sequence of geological events. Data were collected from two experiments to examine ninth graders' abilities for reconstructing a sequence of geological events with the aid of FossilSim. The sample groups in Experiments 1 and 2 were 58 and 11 ninth graders, respectively. The results indicated that the authentic inquiry lesson promoted the development of students' inquiry skills. In addition, FossilSim played a key role in engaging students to apply geological laws, make multi-scale observations, and clarify their ideas about geological time.