Herein, goji berries were pretreated with sodium carbonate (Na2CO3) and then dried via ultrasound-assisted air drying or microwave drying. Water migration and phenolic chemistry of the berries were studied under drying. A three-dimensional ellipsoid water transport model, accounting for porosity and temperature fluctuations, was established to explore the intricacies of the drying mechanism. Generally, microwave drying promoted interior water transport compared to ultrasound drying. Among all the drying methods, MW-240 W exhibited the highest De (from 7.34 × 10−9 to 9.61 × 10−9 m2/s) and kc (6.78 × 10−4 m/s) values. The goji berries received a considerably high and comparable water content gradient between its surface and center along all the drying process within the first 2 s of all the drying treatments. Microwave drying diminished the water content gradient earlier than air drying and ultrasound drying treatments. Furthermore, most correlations observed among phenolics, oxidase activity, and cell wall pectin did not align with the established theories, highlighting the highly nonlinear nature of phenolic chemistry during goji berry drying. This study provides a three-dimensional model to study the mass transfer mechanism of goji berries and analyzes the evolution of polyphenols during the drying process.