We present crustal strain and deformation models for the Sichuan-Yunnan region based on high-precision GPS measurements from 1998 - 2004 using the total least squares method (TLSM). Coordinate errors as well as GPS velocity errors recorded at GPS stations are considered, but only the latter errors are considered using the conventional least squares method (LSM). In addition, the spatial pattern of a given strain field is also likely to be heterogeneous. We investigate two models with a spatially variable strain, the least squares heterogeneous strain model (LS-HSM) and the total least squares heterogeneous strain model (TLS-HSM). Our result shows that estimated strain field parameters are more precise using the TLS-HSM than those by LS-HSM because the fitting to the data is improved, hence the TLS-HSM is preferred. The principal dilation strain rate, principal contraction strain rate, maximum shearing strain rate and surface dilation rate estimated by TLS-HSM in the northwestern Sichuan-Yunnan sub-block are 13.2526 ± 1.2624, -10.8001 ± 2.9826, 24.0527 ± 3.2381, and 2.4525 ± 3.2393 × 10^-9 yr^-1 (with a confidence probability of 95%), respectively, while those in the southeastern Sichuan-Yunnan sub-block are 18.8651 ± 1.8353, -12.0875 ± 1.3926, 30.9525 ± 2.2971 and 6.7776 ± 2.3105 × 10^-9 yr^-1 (and exhibiting similar probabilities), respectively. The results indicate that the sub-blocks play a key role in continental tectonic deformation in the Sichuan-Yunnan region, and that small errors in site coordinates can have a significant impact on strain estimates, especially where sites are close together.