Ultrasound-assisted fluxless brazing of Zr based Bulk metallic glasses (Zr-BMG) joint using Zn-3Al filler metal was performed in this study. The effect of ultrasonic vibration time on the microstructure and mechanical properties of Zr-BMG joints were investigated. Results showed that excellent metallurgic bonding could be obtained in ultrasonically brazed Zr-BMG joints. The interfacial reaction between liquid Zn-3Al filler metal and Zr-BMG substrate showed a mutation characteristic, which could be distinguished into incubation period and acceleration period. In the incubation period, ZnZrAl intermetallic compounds (IMCs) with small ellipsoidal shape were slowly formed and distributed randomly on Zr-BMG surface. However, in the acceleration period, ZnZrAl ellipsoids developed rapidly into a wavy-structured IMCs layer with a thickness of 17 μm, which was comprised of alternate ZnZrAl and ZnZr sublayers. The microstructure evolution of Zn-3Al/Zr-BMG interface was ascribed to the combined effects of acoustic cavitations and Al element controlled interfacial metallurgic reactions. The average shear strength of joint was increased firstly then decreased slightly with increasing ultrasonic vibration time, and a highest strength value of approximately 100 MPa was obtained for joints brazed for 96 s. The shearing failure was inclined to occur at the Zn-3Al/Zr-BMG interface then transferred into the interfacial IMCs layer with increasing ultrasonic vibration time.