A method for controlling temperatures in hot runners of a multi-cavity injection mold, a warning method, and a control system based on those methods are provided, in which a temperature sensor is positioned at the same location as each of the cavities of the mold, one of the cavities is chosen as a standard cavity, and a standard filling time is defined. Besides, in every injection cycle, a calculating and controlling module is to calculate the differences between the standard filling time and the filling times of the cavities, and according to the differences, the temperatures in the hot runners may be adjusted by a temperature-adjusting device and a warning device may be started. So, the volumetric filling of the cavities can be balanced very quickly, the process can avoid fluctuations of external environment so as to reduce the time for product development, and the quality of production can be maintained.