Ultrasonic treatment was firstly found to accelerate both biomass and hydrocarbon productivities of Botryococcus braunii algal cells cultured in the shake flasks. The most effective sonication strategy was to subject the cells to three 5-min ultrasonic treatments at a 4-day interval using a fixed frequency of 40 kHz and power of 240 W, and the ultrasound-treated algal cells showed the highest biomass productivity of 0.043 g L−1 day−1 and the highest hydrocarbon productivity of 13.1 mg L−1 day−1 among all ultrasound treatments tested. The improved productivity was proved to be mainly due to the enhancement of both endogenous indole-3-acetic acid (IAA) biosynthesis and membrane permeability in the ultrasound-stimulated algal cells. The efficient ultrasonic stimulation strategy also showed good performance for the algal culture in a 2-L airlift bioreactor. Together, these results not only illustrate the immense potential for an enhanced understanding on ultrasound-stimulated algal cells but also as provide a powerful process intensification method to improve the biomass and hydrocarbon productivity of B. braunii in practice.