Auditory, which served as one of the five sense systems, play a vital role in human beings’ daily life. Among the many auditory detection techniques, Auditory Brainstem Response (ABR) is widely chosen and studied for its convenience and objectivity. The averaging (Ave) technique is the currently applied method to extract ABR from the EEG signals and is regarded as the gold standard in the clinic. However, the Ave technique is not suitable for noisy condition, like active behavioral condition, which requires the subjects to keep stay during the whole ABR test and is therefore not suitable for newborn. To extract ABR signals from the real active behavioral condition, an adaptive kalman filter (AKF) technique was proposed and systematically investigated from the morphology aspect in two conditions, namely rest and active behavioral (chewing) conditions. The results showed that in rest condition, the ABR signal obtained by the AKF method was highly similar to that of the gold standard method, and the latencies and amplitudes of characteristics waves were also alike. Moreover, we analyzed the latencies and amplitudes of the characteristics waves and CC between the standard ABR and the different method-based ABR. The analyses showed that the AKF had the potential on the extraction of ABR in active behavioral condition. The AKF method provides a new way to robust denoise, and opens a window for ABR acquisition in active behavioral condition, making ABR acquisition in daily life more possible.