In order to better constrain the evolution and petrogenesis of pegmatite, geochemical analysis was conducted on a suite of apatite crystals from the Altay Koktokay No. 3 pegmatite, Xinjiang, China and from the granitic and amphibolitic wall rocks. Apatite samples derived from pegmatite zones show convex tetrad effects in their REE patterns, extremely negative Eu anomalies and non-chondritic Y/Ho ratios. In contrast, chondritic Y/Ho ratios and convex tetrad effects are observed in the muscovite granite suggesting that different processes caused non-chondritic Y/Ho ratios and lanthanide tetrad effects. Based on the occurrence of convex tetrad effects in the host rocks and their associated minerals, we propose that the tetrad effects are likely produced from immiscible fluoride and silicate melts. This is in contrast to previous explanations of the tetrad effect; i.e. surface weathering, fractional crystallization and/or fluid-rock interaction. Additionally, we put forward that extreme negative Eu and non-chondritic Y/Ho in apatite are likely caused by the large amount of hydrothermal fluid exsolved from the pegmatite melts. Evolution of melt composition was found to be the primary cause of inter and intra-crystal major and trace element variations in apatite. Mn entering into apatite via substitution of Ca is supported by the positive correlation between CaO and MnO. Different evolution trends in apatite composition imply different crystallization environments between wall rocks and pegmatite zones. Based on the geochemistry of apatite samples, it is likely that there is a genetic relationship between the source of muscovite granite and the source of the pegmatite.