Stimulus substitution theory is a part of the spectrum of techniques that are identified under the umbrella of classical conditioning. This involves pairing a new stimulus with an already conditioned stimulus (CS).
According to stimulus substitution theory, after pairing the new stimulus with the existing conditioned stimulus it is possible to replace the first CS with the new stimulus. For instance, you have conditioned a rat to respond to a whistle as a signal that it is about to be fed. Then you add a flashing light to the whistle as a signal. After a few training situations you would be able to dispense with the whistle and just use the lights to signal that it is time to eat. You have substituted the light stimulus for the whistle stimulus.