Wilms tumor (WT) is the most common cancer that primarily develops in abdominal solid organ of children. It has no incipient symptom, and the most frequent symptoms are a painless, palpable abdominal mass. Proteomics technology was used to select the differentially expressed proteins of bilateral Wilms tumor (BWT). Ten serum samples of children with BWT were chosen, 20 serum samples of children with unilateral WT (UWT) and 20 serum samples of healthy children were selected, and proteomics technology was used to detect and collect data. Using bioinformatics, the data were analyzed and 10 difference peaks were obtained (P<0.01). Non-linear support vector machine was used to classify and to select the composite pattern with the highest Youdens index, and one differentially expressed protein with m/z of 5,648 kDa was obtained. A significantly high expression in children with BWT was obtained, and the expression intensity was also significantly (3,889.36±1,796.83) higher for children with BWT compared to those with UWT (2,886.81±1,404.65) and healthy children (432.21±730.42). Matrix-assisted laser desorption ionization/time-of-flight ionization/time-of-flight mass spectrometry was used for identification of the peak, and the peak was further identified as apolipoprotein C-III (APO C-III) by western blot analysis. In conclusion, to the best of our knowledge, a differentially expressed protein of APO C-III of BWT was obtained through proteomics technology for the first time, and it is expected to be a new marker for the early diagnosis and prognosis of BWT.