Quantitative studies on the extension and subsidence of the Wanan Basin were carried out based on available seismic and borehole data together with regional geological data. Using balanced cross-section and backstripping techniques, we reconstructed the stratigraphic deposition and tectonic evolution histories of the basin. The basin formed from the Eocene and was generally in an extensional/transtensional state except for the Late Miocene local compression. The major basin extension occurred in the Oligocene and Early Miocene (before ~16.3 Ma) and thereafter uniform stretch in a smaller rate. The northern and middle basin extended intensely earlier during 38.6–23.3 Ma, while the southern basin was mainly stretched during 23.3–16.3 Ma. The basin formation and development are related to alternating sinistral to dextral strike-slip motions along the Wanan Fault Zone. The dominant dynamics may be caused by the seafloor spreading of the South China Sea and the its peripheral plate interaction. The basin tectonic evolution is divided into five phases: initial rifting, main rifting, rift-drift transition, structural inversion, and thermal subsidence.