Calcium oxalate (CaOx) stone is the most common type of kidney stone, with a formation process comprising supersaturation, nucleation, growth, aggregation to crystals, and adhesion on renal tubular epithelial cells. CaOx stones generally lead to renal injury; however, the underlying mechanism remains poorly understood. Accumulating evidence suggests that nanosized materials could induce much greater toxicity than bulk materials with the same components. As aggregation to nanocrystals is necessary to form CaOx stones and nanocrystals have been widely reported to elicit either prodeath or prosurvival autophagy, the aim is to address the precise role of autophagy in CaOx‐ nanocrystal‐induced cytotoxicity. Clinical CaOx stones from patients are collected followed by ball milling. As a result, CaOx nanocrystals significantly reduce renal cell viability in a dose‐ and time‐dependent manner. Further study shows that CaOx nanocrystals possess an autophagy‐inducing capacity and autophagic flux is complete. Autophagy abrogation by specific chemical inhibitor wortmannin or chloroquine obviously attenuates cytotoxicity, strongly suggesting that prodeath autophagy contributes to CaOx nanocrystals‐elicited cytotoxicity. Finally, it is revealed that autophagy is an essential signaling pathway participating in apoptosis regulation. Collectively, the findings demonstrate the role of autophagy in CaOx‐nanocrystal‐elicited cytotoxicity, and harnessing autophagy can be helpful to design promising strategies for attenuating kidney injury in nephrolithiasis.