This article presents a mass sensor based on a 3-degree-of-freedom (DoF) mode localized piezoelectric bulk acoustic wave (BAW) resonator system operating in the contour extensional mode. It features a quality factor of ~4200 under atmospheric pressure at a resonance frequency of ~6.36 MHz. More than three orders of magnitude enhancement (~1700 times) of the normalized mass sensitivity based on the amplitude ratio (AR) change were achieved compared to that based on the frequency shift. The mass resolution thereof was obtained as 1.2 pg (for the AR change output) and 0.727 pg (for the frequency shift output), respectively. Compared with the previously reported mass sensor based on coupled BAW resonators, the presented device achieved an enhanced performance in terms of both quality factor (~2.37 times higher), stability (~100 and ~3.5 times better for the AR change and frequency shift), and mass resolution (~307 and ~2.97 times better for the AR change and frequency shift). Moreover, the stability of the 3-DoF system with the AR change output was enhanced since there was only a ~1.65-fold difference in the mass resolution in terms of the frequency shift and AR change, compared to ~170-fold in the previous study. Furthermore, the novel device operated with a Q-factor of ~305 in deionized (DI) water, demonstrating the considerable potential of such devices for future sensing applications in a liquid environment.