Objective To explore the diagnosis of cystinosis. Methods The clinical and biochemical information, and gene detection results in a child with cystinosis was retrospective analyzed. Results Four-year-old female presented with photophobia and corneal crystal was found by ophthalmic examination at 2 years old, bilateral kidney stone was found, accompanied by development delay and rickets at 3 years old. Gas chromatography analysis in urine showed that a variety of amino acids were increased, and urine sugar and urinary micro-protein were also increased, which were in accordance with fanconi syndrome. The blood free carnitine was decreased, ester acyl carnitine spectrum was normal, and multi-amino acids such as lysine, valine and arginine were decreased. Gene analysis showed a homozygous mutation of c.696C ＞ G (p.323 N ＞ K) in CTNS gene, which was a known mutation. Both her parents were carrier of heterozygous mutation of c.696C ＞ G in CTNS gene. Conclusion Child with kidney stone, renal damage, combined by multi-system damage such as eyes, bone, and thyroid should be paid attention to identify the cystinosis.