A resource survey from 2013 to 2015 found white berries in Qinghai Province. The phenotype and main active compounds were determined in the two berries at three stages (Ⅰ～Ⅲ) to compare the differences. The results showed that: (1) the shape of white fruit and black fruit were the same, and there was no significant difference in volume and mass. (2) Anthocyanin content in black fruit at the second period up to 17.18 mg/g fresh weight and in white fruit was extremely low in all three periods. The lack of anthocyanin caused the appearance of white fruits. (3) The total polyphenol, polysaccharides and vitamin E were found in black and white fruits, and the content all of them reached the highest at stage Ⅱ, Ⅲ. Although the content of these active substances in white fruits was considerable, they were significantly lower than that of black fruits in all developmental stages. (4) Ten of the seventeen mineral elements (B, Ca, Li, Mg, Mn, Na, Si, K, Zn and Al) are dominant in the white fruit. This study provided basic data for the variety selection, nutrition value evaluation and adaptability of white fruit from Lycium ruthenicum Murr.