A novel ultrasound-assisted freezing system that can generate orthogonal ultrasound was developed, and the effects of single/dual-frequency orthogonal ultrasound-assisted freezing as compared with single direction ultrasound-assisted freezing on the quality of potatoes were investigated. Inner links between ultrasonic intensity, cavitation yield, and potato quality attributes including drip loss, hardness, total calcium content, l-ascorbic acid content, total phenolic content and microstructure were revealed. Besides, principal component analysis (PCA) was used to analyze and visualize the quality variation of potatoes before and after freezing. Results showed that orthogonal ultrasound could predominately decrease drip loss and enhance hardness by increasing the freezing rate and shortening the total freezing time. Microstructure observation indicated that dual-frequency orthogonal ultrasound-assisted freezing endowed potatoes with the finest pores and the plumpest tissue, which was in agreement with the PCA result. This study announces the great potential of the dual-frequency orthogonal ultrasound-assisted freezing technique in promoting the freezing quality.