The present invention relates to systems and methods for heating intake air during cold HCCI operation. A system for controlling intake airflow of an engine includes a mode determination module, a throttle valve control module, and a valve actuation module. The mode determination module generates a mode signal based on an engine speed signal and an engine load signal. The mode signal indicates one of a spark ignition mode and a homogeneous charge compression ignition mode. The throttle valve control module generates a valve control signal based on the mode signal, a temperature signal, and a plurality of valve position signals that indicate positions of first and second throttle valves. The throttle valve control module controls the positions of the first and second throttle valves to regulate flow rates of intake air into an intake manifold of the engine via a heat exchanger based on the valve control signal. The valve actuation module actuates the first and second throttle valves based on the valve control signal.