High-temperature thin film heat flux sensors have been fabricated by growing c-axis tilted epitaxial Ca3Co4O9 (CCO) thin films on 5° vicinal cut LaAlO3 (001) single crystal substrates. The layered structure of Ca3Co4O9 yields the significant Seebeck coefficient anisotropy between the ab-plane and c-axis, which could generate a voltage of the heat flux sensor via the transverse thermoelectric (TTE) effect of thin films. A sensitivity of 27.7 μV/(kW/m2) has been determined in such 5° tilted Ca3Co4O9 thin films, which is much larger than other reported ones based on the TTE effect from various materials. After a thermal treatment at 900 °C in air for 10 min, the sensitivity of such heat flux sensors is almost non-variable, which indicates that the temperature resistance of the CCO-based TTE heat flux sensor is as high as 900 °C. In addition, a fast response time of 45 μs has been identified in such CCO-based TTE heat flux sensors. These results demonstrate that the CCO is a promising candidate to manufacture the TTE heat flux sensors with the superiorly comprehensive performance, including the high temperature resistance, high sensitivity, and fast response.