The ability to manipulate quantum systems lies at the heart of the development of quantum technology. The ultimate goal of quantum control is to realize arbitrary quantum operations (AQUOs) for all possible open quantum system dynamics. However, the demanding extra physical resources impose great obstacles. Here, we experimentally demonstrate a universal approach of AQUO on a photonic qudit with the minimum physical resource of a two-level ancilla and a log_{2}d-scale circuit depth for a d-dimensional system. The AQUO is then applied in a quantum trajectory simulation for quantum subspace stabilization and quantum Zeno dynamics, as well as incoherent manipulation and generalized measurements of the qudit. Therefore, the demonstrated AQUO for complete quantum control would play an indispensable role in quantum information science.