As a part of the energy transmission chain, gearboxes are considered as important components in rotating machines, and the gearbox failure results in costly economic losses. Therefore, it is necessary to detect the appearance of incipient gearbox faults by implementing an appropriate detected model. The incipient failure characteristics of the gearbox are weak and hidden in a set of time-varying series signals the vibration signals, which is difficult to effectively extract under the background of strong noise. The PCA method is not effective in detecting weak fault features in time-varying signals, so this paper proposes a method based on Deep Recursive Dynamic Principal Component Analysis (Deep RDPCA) to detect incipient faults in gearboxes. The proposed approach is modeled via both the deep decomposed theorems and time-varying dynamic model based on traditional PCA to extract characteristic of time-varying and weak fault information under the background of strong noise. The proposed method could get a better real-time reflection for changed system by introducing “Moving Window” technologies, so that the incipient fault of gearbox could be detected accurately, too. Finally, the effect of Deep RDPCA-based fault diagnosis is compared with the results of PCA, DPCA, RDPCA, Deep PCA, and Deep DPCA methods. It is concluded that the proposed method can effectively capture the time-varying relationship of process variables and accurately extract the weak fault characteristics in the vibration signal, which effectively improves the fault detection performance.