A system for controlling low-temperature starting of a fuel cell vehicle includes a high-pressure hydrogen flow control valve controlling a flow of hydrogen supplied to a fuel cell stack. A fuel cell controller is configured to change and control an opening rate of the high-pressure hydrogen flow control valve when an internal temperature of the fuel cell stack is a reference value or less. When the opening rate of the high-pressure hydrogen flow control valve decreases, a pressure of the hydrogen passing through the high-pressure hydrogen flow control valve decreases to increase a temperature of the hydrogen which is supplied to the fuel stack.