Based on temperature logs of 117 boreholes and thermal conductivity of 119 rock samples, the first group of 35 heat flow data in the Junggar Basin are presented. The thermal gradients vary between 11.6 and 26.5°C/km, and the thermal conductivity changes from 0.17 to 3.6 W/mK. Heat flow ranges from 23.4 to 53.7 mw/m2 with a mean of (42.3±7.7) mW/m2. The heat flow pattern shows that heat flow is higher in the uplifts and lower in the depressions. The factors affecting the heat flow and its distribution include basin type, basement structure, sediment thickness, radioactive heat generation, etc. The overall low present-day heat flow in the Junggar Basin reflected its tectonothermal evolution characterized by lithospheric thickening, thrust and fault at shallow crust as well as consequently quick subsidence during the Late Cenozoic.