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The long gamma-ray burst GRB 161017A was detected by Fermi and Swift, and its afterglow was observed by the MITSuME 50-cm optical telescope promptly about 50 s after the burst. Early optical observations revealed that the optical lightcurve exhibits a plateau and rebrightening in the early afterglow phase about 500 and 5000 s after the trigger, respectively. By investigating the behavior of the spectral and temporal flux variation, it was found that the plateau and re-brightening cannot be explained in the context of the simple standard afterglow model. These observational features can be explained with two independent refreshed shocks, which indicate the long-acting central engine. We evaluated the physical parameters of the subsequent shells, and we then determined the kinetic energy ratio of the two colliding shells to the leading shell to be roughly 1 and 8, respectively. In addition, two prominent X-ray flares about 200 s after the trigger may be signatures of delayed ejections of the energetic jets responsible for the refreshed shocks. Such late activity of the central engine and X-ray flares play a crucial role in understanding the mechanisms for jet formation and photon emission.