Tectono-thermal modeling of rift basin is to calculate the thermal and subsidence history of a rift basin during its formation and evolution on a lithosphere scale, which links tectonic and thermal developments perfectly. However, most extension models have the following problems: assuming the lithosphere to be 125 km thick initially, ignoring heat convection in the asthenosphere, fixing the upper boundary and rarely including thermal effects of sediments when calculating rift flank uplifts. Some effects on the tectono-thermal modeling are discussed, including the initial crustal and lithosphere thicknesses, the convection of asthenosphere and the upper boundary of the model. We also calculate the differences of rift flank uplift between water and sediment loaded models.The tectono-thermal modeling is based on a two-dimensional non-instantaneous extension model using the finite-element method in the Lagrangian system. By solving the heat conduction equation, the thermal and tectonic subsidence histories of the basin are modeled simultaneously.The results are as follows: (1) Initial crustal and lithospheric thicknesses have great influence on tectonothermal modeling, especially on the tectonic subsidence. (2) Compared to the model ignoring heat convection in the asthenosphere, this model predicts slower tectonic subsidence and thermal decay rates, and significantly higher temperature from the lower crust to the bottom of the model. (3) The fixed or moving upper boundary during the modeling influences the calculated heat flow and tectonic subsidence in the thermal subsidence phase, and has remarkable effects on the temperature field. The effect increases with the increasing of stretching factor. (4) Rift flank uplift of the water-loaded model would disappear within millions of years while the uplift would be stable at a certain value for the sediment-loaded model.In cases that the initial crustal and lithospheric thicknesses are uncertain, the optimum initial thicknesses for crust and lithosphere can be determined when the calculated heat flow, Moho depth and lithospheric thickness fit observed values best. Pure heat conduction and pure heat convection in the asthenosphere are two limiting cases for extension models. Within the rheological boundary layer, heat is transferred by both conduction and convection. For strongly extensional areas, using the fixed upper boundary model would generate large calculation errors, especially in the temperature field. The thermal effect of sediment cannot be ignored when calculating the rift flank uplift.