The molecular and physiological mechanisms of how rare earth oxide nanoparticles (NPs) alter radish (Raphanus sativus L.) taproot formation and cracking were investigated in the present study. We compared plants that received suspensions of 10, 50, 100, 300 mg L−1 of La2O3 NPs, 300 m L−1 La2O3 bulk-particles (BPs), 0.8 m L−1 La3+, or only water for six days during their tuber formation period. 100 and 300 mg L−1 La2O3 NPs exposure decreased storage root biomass by 38% and 60%, respectively, and they both induced visible root cracking. Physiological analyses showed that La2O3 NPs exposure (>100 mg L−1) significantly inhibited leaf net photosynthetic rate, cell wall pectin synthesis of both storage root epidermis and xylem parenchyma tissues, but increased the contents of cellulose and hemicellulose 1 in root epidermis cell walls. Moreover, transcriptome analysis further found that La2O3 NPs changed root cell wall structure by down-regulating core genes involved in cell wall pectin and IAA biosynthesis, which coincided with the observed La2O3 NPs-induced root cracking. Our results revealed the molecular mechanisms related to cell wall carbohydrate metabolism in response to NPs stress, providing a step forward for understanding the causes of NPs phytotoxicity on edible plant taproot formation and cracking.