A method of operating a microchannel reactor, in which a reaction channel is formed, includes generating a reaction product by causing a chemical reaction in a raw material fluid while causing the same to flow through a reaction channel. If the flow rate of the raw material fluid and/or the reaction product fluid flowing through a reaction channel decreases, a fluid which is inert to the raw material fluid and the reaction product is mixed into the fluid flowing through the reaction channel, in a flow rate corresponding to the decreased flow rate and at a position downstream of the introduction position of the raw material fluid into the reaction channel.