My two year old son has been extremely congested and coughing very badly, but only at night.?

??sleeping envt?? Night only cough is often triggered by allergens or iritants causing postnasal drainage, dry heat or mild uncontrolled asthma. Talk with your dr about this. Pillow & matress encasements can reduce dust mite exposure.Humidifiers, head up bed angle, air particle filters etc may all help.
Elevate bed. Slightly elevating the head of the bed can allow the mucous to drain more easily. He could also be allergic to dust mites which are usually found in the bed.