Incipient faults are difficult to be detected due to the intrinsic fault tolerance of traditional controller, but it should be eliminated as soon as possible before it deteriorates with time into something more serious. As a consequence of an intrinsic inability to assess whether a fault occurs based on output residual, the existing detection methods are failure for incipient fault. So the aim of active fault detection (AFD) is to make the system be unstable when incipient fault has occurred, which drives rapid fault detection. The fault-tolerant control (FTC) is designed to maintain the system stable and eliminate the fault impact without shutting the process down even if faults occur. In this paper, the Youla–Jabr–Bongiorno–Kucera (YJBK) parameter is employed to build the AFD and the FTC based on the relationship analysis between the fault and the dual YJBK parameter. A new structure of the tolerant controller parameter for FTC is designed, named as partial active FTC (PAFTC). PAFTC is dependent upon the fault detection information but not the fault size considering the parameter fault with unknown size and known form. A unified operation architecture for AFD and PAFTC with different YJBK parameters for incipient faults is proposed. Some illustrative examples are given to indicate the effectiveness of the proposed unified operation architecture.