Purpose To investigate the alterations of trace elements levels in aqueous humor of patients with cytomegalovirus retinitis (CMVR). Methods A total of 15 eyes of 11 patients with CMVR and 24 eyes of 24 patients with senile cataract as control group were enrolled. Aqueous humor samples were assessed for calcium (Ca), potassium (K), magnesium (Mg), sodium (Na), phosphorus (P), titanium (Ti), vanadium (V), chromium (Cr), manganese (Mn), iron (Fe), nickel (Ni), copper (Cu), zinc (Zn), selenium (Se), strontium (Sr), and lead (Pb) by using inductively coupled-plasma-mass-spectrometry. Meanwhile, we examined the concentration of the CMV DNA load by using PCR and the concentration of interleukin (IL)-8 by using a cytometric bead array. Results In patients with CMVR, the aqueous humor levels of P and Cu were significantly higher than those of controls (p < 0.001, p < 0.001, respectively). However, levels of K and Mg were significantly lower in patients with CMVR (p < 0.001, p < 0.001, respectively). The Spearman correlation test showed that the concentration of IL-8 in the aqueous humor was significantly associated with the aqueous level of Cu (p = 0.009, r = 0.646) and Se (p = 0.031, r = 0.558). In addition, the concentration of CMV DNA load in the aqueous humor was significantly associated with the aqueous level of Ca (p = 0.027, r = −0.568), Mn (p = 0.020, r = 0.593), and Cu (p = 0.043, r = 0.527). Conclusions Our preliminary results demonstrated that the abnormal aqueous levels of trace elements (P and Cu) in CMVR patients. Thus, the roles of trace element changes in the development of CMVR and the influence of intraocular trace element for the prognosis of CMVR warrant further investigations.