Microalgae have been widely employed in water pollution treatment since they are eco-friendly and economical. However, the relatively slow treatment rate and low toxic tolerance have seriously limited their utilization in numerous conditions. In light of the problems above, a novel biosynthetic titanium dioxide (bio-TiO2NPs)—microalgae synergetic system (Bio-TiO2/Algae complex) has been established and adopted for phenol degradation in the study. The great biocompatibility of bio-TiO2NPs ensured the collaboration with microalgae, improving the phenol degradation rate by 2.27 times compared to that with single microalgae. Remarkably, this system increased the toxicity tolerance of microalgae, represented as promoted extracellular polymeric substances EPS secretion (5.79 times than single algae), and significantly reduced the levels of malondialdehyde and superoxide dismutase. The boosted phenol biodegradation with Bio-TiO2/Algae complex may be attributed to the synergetic interaction of bio-TiO2NPs and microalgae, which led to the decreased bandgap, suppressed recombination rate, and accelerated electron transfer (showed as low electron transfer resistance, larger capacitance, and higher exchange current density), resulting in increased light energy utilization rate and photocatalytic rate. The results of the work provide a new understanding of the low-carbon treatment of toxic organic wastewater and lay a foundation for further remediation application.