The effects of the reactivity of a crosslinking agent on the microphase-separated structure of sequential interpenetrating polymer networks are analyzed with a Monte Carlo simulation technique. The simulation results showed that the maximum structure factor decreases with an increasing crosslinking rate. However, the maximum structure factor increases when the crosslinking rate is increased further. This behavior is explained by a competition between the phase separation and the restriction of chain mobility due to the increase in molecular weight. In addition, there exists a chain length where the chain motion is the most restricted when crosslinks are formed.