The influences of citrus aurantium juice (CAJ) immersion and resonant vibration assisted by the immersion on the instrumental properties, cooking loss, vibrated weight gain of supraspinatus (SS), quadriceps femoris (QF) and longissimus thoracis (LT) muscles from yak carcasses were investigated, as well as the collagen characteristics, pyridinoline cross-links, myofibrillar MFI. In the circumstance of CAJ concentration of 1% and the ratio of meat to liquid 1:2, the shear force of SS and QF were significantly decreased by 20.3% and 20.2% (P < 0.05), and cooking loss significantly decreased by 17% and 23% (P < 0.05), respectively, compared to the control. At this combination of the concentration and the ratio of meat to liquid, the total collagen contents of SS and QF were significantly decreased by 23% and 18%, the collagen heat solubility 1.4 times and 1.5 times that of the raw meat (P < 0.05), respectively. At the pH value closed to the pI of myofibrillar proteins, the immersion assisted resonance with the amplitude of 2 mm and vibration duration of 1 h made the LT shear force to be decreased by 12%, 7.8% and 10.9% than the control, 0.5 h and 1.5 h of vibration duration (P < 0.05), respectively. Furthermore, the ultrastructure in LT gave rise to obvious alteration due to the CAJ immersion and its assisted resonance. The present study has confirmed again that the resonance does cause meat tenderization by means of destroying the integrity of the M-band structure in sarcomere.