The two-factor authentication (2FA) has become pervasive as the mobile devices become prevalent. Existing 2FA solutions usually require some form of user involvement, which could severely affect user experience and bring extra burdens to users. In this work, we propose a secure 2FA that utilizes the individual acoustic fingerprint of the speaker/microphone on enrolled device as the second proof. The main idea behind our system is to use both magnitude and phase fingerprints derived from the frequency response of the enrolled device by emitting acoustic beep signals alternately from both enrolled and login devices and receiving their direct arrivals for 2FA. Given the input microphone samplings, our system designs an arrival time detection scheme to accurately identify the beginning point of the beep signal from the received signal. To achieve a robust authentication, we develop a new distance mitigation scheme to eliminate the impact of transmission distances from the sound propagation model for extracting stable fingerprint in both magnitude and phase domain. Our device authentication component then calculates a weighted correlation value between the device profile and fingerprints extracted from run-time measurements to conduct the device authentication for 2FA. Our experimental results show that our proposed system is accurate and robust to both random impersonation and Man-in-the-middle (MiM) attack across different scenarios and device models.