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Cellulose nanocrystals (CNCs) were successfully fabricated from waste pueraria root residue after starch extraction via the phosphoric acid hydrolysis method by a series of chemical treatment processes including ultrasonic washing, pectin elimination, bleaching, alkali boiling, and phosphoric acid hydrolysis. The high aspect ratio of CNCs with a crystallinity index of 60 ± 4.10% was observed by X-ray diffraction (XRD) and transmission electronic microscopy (TEM). The TEM results showed that CNCs were rod-like particles with 100–330 nm in length and 2 to 6 nm in width. The average aspect ratio of the CNCs was 40 ± 10. The XRD results also indicated that the crystalline structure of CNC was cellulose I, compared to that of MCC with the crystallinity index declining from 60 ± 4.10% to 48 ± 0.37%. The FTIR spectra showed the resulting samples were the cellulose species. Interestingly, stable colloidal suspensions were determined by the zeta potential measurement. The thermal properties of CNCs were investigated by thermogravimetric analysis, revealing that CNCs exhibited lower thermal stability compared to those of MCC and the raw pueraria root residue. This study provides a cost effective method and mild process conditions for preparing CNCs from waste pueraria root residue.