The number of distributed renewable energy sources of integrated energy systems (IESs) are increasing. The volatility of renewable energy exacerbates active power imbalances and increase frequency deviations in power systems. This work proposes a decomposition prediction fractional-order active disturbance rejection control deep Q network (DPFOADRCDQN) to control each generator of IESs more accurately and to reduce systemic frequency fluctuation. According to the fluctuation size of frequency deviation, the sub-signal obtained after the prediction of the modal decomposition of frequency deviation is classified into big fluctuating signals and small fluctuating signals; fractional-order active disturbance rejection control (FOADRC) controls small fluctuating signals; deep Q network (DQN) controls big fluctuating signals. Frequency deviation signals in complex power systems with a large percentage of renewable energy have higher smoothness after modal decomposition, FOADRC can efficiently follow the small fluctuating signals, and DQN can learn the rich data features in the big fluctuating signals and give precise control commands. The DPFOADRCDQN, proportional-integral-derivative, Q-learning, fuzzy control, and the previous state-of-the-art reinforcement learning are simulated in IESs where the renewable energy generators output is 0 %, 20 %, 40 %, 65 %, and 80 % of all generators output, the results show the average frequency deviation, total generation cost, and carbon emission cost are at least 42.7 %, 0.92 %, and 0.93 % smaller than the comparison algorithm, respectively.