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This paper investigates the clocking effect in subsonic compressor element stages and the influence of design parameters on the flow mechanism. We focus on the relationship between the wake-induced separation loss and wake mixing loss and the unsteady mechanism in the wake flow process without considering the transition through several steady and unsteady numerical simulations aimed at a series of subsonic compressor element stages. The simulation results indicate that the performance difference at various indexing positions depends on the relationship between wake mixing loss and wake-induced separation loss for different compressor designs and operating conditions. Furthermore, the pressure transport caused by the negative jet of the Stator 0 wake in Rotor 1 creates a local acceleration region called SFAF, and a decrease in its absolute flow angle reduces the Stator 1 separation. Sufficient rim work of the rotor at highly loaded operating conditions is the basis for generating an effective SFAF. Furthermore, the fore-loading blade of Rotor 1 significantly reduces suction surface pressure drop, and a small angle between the stagger angles of Stator 0 and Rotor 1 increases the unsteady rotor load caused by the upstream wake to the total rotor load, both of which enhance SFAF.