Thalamocortical connectivity plays a vital role in brain function. The anatomy and function of thalamocortical networks have been extensively studied in animals by numerous invasive techniques. Non-invasively mapping thalamocortical networks in humans has also been demonstrated by utilizing resting-state functional magnetic resonance imaging (rsfMRI). However, success in simultaneously imaging multiple thalamocortical networks in animals is rather limited. This is largely due to the profound impact of anesthesia used in most animal experiments on functional connectivity measurement. Here we have employed an awake animal imaging approach to systematically map thalamocortical connectivity for multiple thalamic nuclei in rats. Seed-based correlational analysis demonstrated robust functional connectivity for each thalamic nucleus in the cortex, and the cortical connectivity profiles revealed were in excellent accordance with the known thalamocortical anatomical connections. In addition, partial correlation analysis was utilized to further improve the spatial specificity of thalamocortical connectivity. Taken together, these findings have provided important evidence supporting the validity of rsfMRI measurement in awake animals. More importantly, the present study has made it possible to non-invasively investigate the function, neuroplasticity and mutual interactions of thalamocortical networks in animal models.