The Okinawa Trough (OT) is a back‐arc basin located in the eastern edge of the Eurasian Plate. The stage of back‐arc spreading and the exact crustal thickness of the OT are still controversial. To determine the crustal nature and lithospheric structure of the OT, the Moho discontinuity depth of the OT is calculated through the Parker–Oldenburg iterative inversion method based on the Bouguer gravity anomaly data in this article. The result shows that the crustal thickness of the OT is 15–27 km, thinner than those of the typical continental crust, and thicker than those of the normal oceanic crust. In this study, the formation and evolution of marginal basins or back‐arc basins is divided into four stages based on the crustal thickness of the basin. By comparing crustal thickness and heat flow of typical marginal basins located in global passive continental margins and continental rift, it can be inferred that the OT is at a stage later than continental drift. We suggest that the southern and middle OT are at the early stage of back‐arc spreading, while the northern OT is still at the ocean–continent transitional stage. There may have been initial oceanic crust developed at the spreading center in the southern OT. The tomographic images of the OT show that there is low‐velocity anomalous mantle beneath the OT, providing deep geophysical evidence for back‐arc spreading of the OT.