This work was aimed to optimize the formulation of phase change material nano-emulsions by ultrasonic emulsification that has not been investigated systematically. The optimization was performed using response surface methodology on two response parameters, average droplet size and apparent viscosity, and three independent variables including ultrasonic amplitude (X1), treatment time (X2), and surfactant content (X3). The significance of three variables on both droplet size and apparent viscosity followed the order of X3 > X1 > X2. At the optimal variable levels (X1 = 58 %; X2 = 9 min; X3 = 8 wt%), the droplet size of 118.2 nm and apparent viscosity of 7.3 mPa·s were predicated by the regression model and also well verified by experiments. The 25 wt% phase change nano-emulsion formed by ultrasonication exhibited the best emulsion stability and the lowest apparent viscosity compared with those formulated by high-energy rotor-stator homogenizer and low-energy method of phase inversion temperature. In addition, the rheological behavior associated with the average droplet size and the solid/liquid state of phase change material was illustrated numerically for the first time. In general, a threshold of 170–180 nm was found for the transition of liquid-in-water emulsions from a shear-thinning non-Newtonian fluid to a Newtonian fluid in the shear rate range of 0.6–73 s−1. All solid-in-water suspensions showed shear-thinning fluid behavior, though the shear-thinning degree was dramatically reduced to a flow behavior index of about 0.95 as the particle size was below 100 nm. These findings may be useful for designing high-performance phase change material nano-emulsions with long service life, high energy storage capacity, and low pumping power consumption for applications.