Objectives To investigate the diagnostic value of tumor markers and brain MR in children with intracranial germ cell tumors. Methods From March 2010 to March 2018， a total of 92 cases of children suspected of germ cell tumor treated in Beijing Tiantan Hospital affiliated to Capital Medical University were selected. The children completed brain magnetic resonance（ MR） imaging， as well as cerebrospinal fluid and serum alpha-fetoprotein（ AFP）， Human chorionic gonadotropin β subunit（ β-hCG）， and placental alkaline phosphatase（ PLAP） expression level monitoring. With the pathological examination of diseased brain tissue as the diagnosis "gold standard"， brain MR and cerebrospinal fluid and serum tumor markers were evaluated for diagnostic value in children with intracranial germ cell tumors. Results The diagnostic sensitivity of brain MR in children with intracranial germ cell tumors was 53.13%（ 17/32）， the specificity was 90.00%（ 54/60）， and the positive coincidence rate was 77.17%（ 71/92）. The positive predictive value was 73.91%（ 17/23）， and the negative predictive value was 78.26%（ 54/69）. The diagnostic sensitivity of serum AFP， β-hCG and PLAP in children with intracranial reproductive tumors was 81.25%（ 26/32）， the specificity was 51.67%（ 31/60）， and the positive coincidence rate was 61.96%（ 57/92）. The positive predictive value was 47.27%（ 26/55）， and the negative predictive value was 83.78%（ 31/37）. The diagnostic sensitivity of cerebrospinal fluid AFP， β-hCG and PLAP in children with intracranial germ cell tumors was 87.50%（ 28/32）， specificity was 56.67%（ 34/60）， and the positive coincidence rate was 67.39%（ 62/92）. The positive predictive value was 51.85%（ 28/54） and the negative predictive value was 89.47%（ 34/38）. The diagnostic sensitivity and negative predictive value of serum， cerebrospinal fluid AFP， β-hCG and PLAP were significantly higher than those in brain MR in the diagnosis of children with germ cell tumors（ P＜0.05）； The specificity， positive coincidence rate and positive predictive value were significantly higher than those of serum， cerebrospinal fluid AFP， β-hCG and PLAP（ P＜ 0.05）. Conclusions The tumor markers have high diagnostic sensitivity in children with intracranial germ cell tumors. The brain MR has high diagnostic specificity in children with intracranial germ cell tumors. Both methods have diagnosis advantages and disadvantages.