Ge/SiO2 direct wafer bonding by O2-plasma pretreatment was investigated. The bonding interfaces of Ge/SiO2 low temperature direct wafer bonding were characterized by transmission electron microscopy. The perfectly atomic level Ge/SiO2 bonding was achieved after a 1500C annealing for 60 hours. The excessive O2-plasma exposure resulted in micro-crack formation close to the bonding interface in Ge. A model involved micro-crack formed in Ge was proposed. Our experiments, for the first time, demonstrated that a perfectly seamless bonding of Ge/SiO2 by O2-plasma pretreatment depends not only on optimal O2-plasma pretreatment time but also on the manner of the raised annealing temperature to enhance the bonding strength. A slowly ramping rate heating is crucial to accomplish perfectly seamless Ge/SiO2 wafer bonding apart from an optimal O2-plasma exposure time chosen.