In ethylene production units, the acetylene side product is converted into additional C2H4 over a palladium–carbon fixed bed reactor, in which the catalyst activity is affected by the formation of green oil impurities. We determined the optimal dynamic operating conditions for two reactors in series undergoing catalyst deactivation while maintaining the selectivity and conversion rate. The optimal switching periods for the reactors were investigated with dynamic optimization of the hydrogen input and inlet temperature with the incremental feature. Control vector parametrization was used to transform this dynamic problem into a finite-dimensional nonlinear programming problem. An incremental-encoding differential evolution with constraint ranking-based mutation operator (IEDE-CRMO) was proposed based on the reaction selectivity and catalyst activity variation to meet certain requirements of the control variables and to solve a complex industrial process. The IEDE-CRMO method was applied in an industrial C2 hydrogenation tandem reaction process, and results showed improvement in overall operation efficiency.