Crustal deformation history in the Jianchuan basin of northwestern Yunnan Province since the Tertiary is studied through analyses of strata, folding and variations of faulting modes. The result shows that a nearly NS trending fold formed in the Baoxiangsi group (Eb), with dextral thrust on the main fault along the NNE directed basin rim in the early Eocene. Since the Miocene, the fold in the Shuanghe group (N1s) stroke in NE when the main fault on the basin rim changed into sinistral thrust. After the Pliocene (N2Q), the Jianchuan block experiences extension and rifting, with differential crust uplift and normal faulting on the basin rim, as well as intrusion of the upper Pliocene trachyte through fissures. The fission track (FT) dating indicates that the folded Shuanghe group (N1s) is of age15.8±1.8Ma, sinistral thrust on the main fault of the basin rim occurred at 5.4±1.1Ma, later faulting at 1.6±0.7Ma, and the ages of uplifted Jianchuan group (N2j) and upper Pliocene trachyte fall in 2.4±0.85Ma~3.1±.5Ma. These data suggest that the nearly EW directed compression on the basin was at 15Ma B.P, NW directed compressive motion occurred in 15~5.4Ma B.P., and the later extension and normal faulting began 5.4Ma B.P. and culminated in 1.5~1.6Ma B.P. It means that the crustal deformation of the study area was nearly EW directed compression in the early Eocene, changed into NW directed compression in the Miocene, and transformed into extension and rifting since the Pliocene. Such a process of crustal deformation is presumably associated the push of the Indian plate, uplift of the Tibetan plateau and southeastward flow of the plateau material.