Structure formation during high‐temperature reactive blending of randomly functionalized poly‐disperse backbone polymers (such as polyethylene) with end‐functionalized graft polymers (such as polyamide 6) forming co‐continuous nanostructured microphases was investigated by means of MC simulations using the bond fluctuation algorithm. We compared reacted and non‐reacted systems under the same conditions. For the non‐reacted system at low temperatures, phase separation was observed. In the system with grafting reactions, macroscopic phase separation was inhibited even if the consumption of reactive sites was only 50%. The calculated structure factor indicates a distinct difference between the two simulation states in accordance with the 3D visualization of the system and the box‐counting method.