Although perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) have been identified in milk and dairy products in many regions, knowledge on their occurrence in Xinjiang (China) is rare. This study was conducted to measure the levels of PFOA and PFOS in milk and yogurt from Xinjiang and to investigate the average daily intake (ADI) of these two compounds. PFOA and PFOS levels were analyzed using ultrasonic extraction with methanol and solid-phase extraction followed by liquid chromatography–mass spectrometry. Retail milk and yogurt samples present higher detection rates (39.6% and 48.1%) and mean concentrations (24.5 and 31.8 ng/L) of PFOS than those of PFOA (33.0% and 37.0%; 16.2 and 22.6 ng/L, respectively). For raw milk samples, only PFOS was detected. The differences in the levels of the two compounds between samples from the north and south regions were observed, and northern regions showed higher pollution levels than southern regions. On the basis of the retail milk measurements and consumption data, the ADIs of PFOA and PFOS for Xinjiang adults were calculated to be 0.0211 and 0.0318 ng/kg/day, respectively. Furthermore, the estimated intakes of PFOA and PFOS varied among different groupings (age, area, gender, and race) and increased with increasing age. Relevant hazard ratios were found to be far less than 1.0, and this finding suggested that no imminent health damages were produced by PFOA and PFOS intake via milk and yogurt consumption in the Xinjiang population.