Wax precipitation damage caused by cold water injection or temperature reduction is very commonly seen in the development of waxy crude oil reservoirs. Various methods for eliminating wax precipitation damage have been studied by many scholars, such as injecting hot water, artificial fracture, and using chemical dewaxing agents. However, the effects of nanoemulsion on wax crystals and enhanced oil recovery (EOR) have not yet been systematically studied. This study used core displacement system based on nuclear magnetic resonance (NMR) to investigate the effect of nanoemulsion on the EOR in low-permeability, waxy oil reservoirs. Some influencing factors such as injection water temperatures, core permeability, fractured/unfractured core, and nanoemulsion concentration conditions have been investigated. Meanwhile, the wax crystal morphology and quantity have been studied before and after using nanoemulsion using a polarizing microscope. The main conclusions are as follows: (1) After injecting 60 °C hot water, the recovery can be increased from 19.36% to 32.82%, which can alleviate wax deposition damage to a certain extent. (2) Enhancing core permeability or using fractured cores can increase the flow capacity of displacement fluid within the core and enhance waxy crude oil recovery. The EOR after improving core permeability is 10.22%, while the EOR of the fractured core is 26.24%. (3) Nanoemulsions can dissolve wax crystals in waxy crude oil and inhibit their formation to achieve EOR. The crude oil recovery at nanoemulsion concentrations of 0.1, 0.5, and 1.0 wt% were 34.84%, 38.24%, and 42.85%, respectively. (4) The use of nanoemulsion can reduce the number, area ratio, and fractal dimension of wax crystals, thereby mitigating wax deposition damage. Using a 1 wt% of nanoemulsion, the area ratio of wax crystals decreased from 47.25% to 16.67%, and the number of wax crystals decreased from 1309 to 496