To provide a control device for a variable valve system, protecting the variable valve system from a trouble such as malfunction resulting from soot in engine oil.

When the concentration of soot in the oil for an engine 2 detected by a sensor 4 is a concentration value to possibly cause a trouble of the variable valve system 3, an ECU 1 changes over the variable valve system 3 into a starting mode and then prohibits the change-over of the variable valve system 3. Thus, the change-over operation of a low/high speed cam of the variable valve system 3 is prevented to protect the variable valve system 3 from the trouble.