Rosa canina L. (Rosaceae), commonly known as the rose hip, is originated from Europe, Africa, and Asia with a long history in medicinal applications. This study aimed to analyze the morphological traits, fatty acids profile, and content of phenolic compounds, anthocyanins, vitamin C, total carotenoid, total phenol, total flavonoid, and antioxidant activity of the fruits of eleven Iranian R. canina ecotypes (RCEs). The highest coefficient of variation was obtained in 1000 seed weight (46.57%). The seed oil varied from 8.08 ± 0.17% to 16.91 ± 0.35%. Linoleic (35.41 ± 0.78% to 49.59 ± 0.96%) and eicosanoic (17.67 ± 0.06% to 25.36 ± 0.54%) acids were the predominant fatty acids in the studied samples. The anthocyanin content in the fruits was ranged from 0.98 ± 0.03 to 4.41 ± 0.04 mg cyanidin 3-glucoside/100 g of dry weight (mg C3G/100 g DW). The high content of vitamin C (103.51 ± 1.24–419.70 ± 3.12 mg/100 g DW), total carotenoid (111.22 ± 0.78–206.98 ± 1.25 mg β-carotene equivalents per g of dry weight (mg β-CARE/g DW)), total phenol (52.87 ± 0.82–104.52 ± 0.23 mg GAE/g DW), and total flavonoid (14.20 ± 0.12–25.18 ± 0.47 mg RE/g DW) were observed in the studied samples. Catechin (20.42 ± 0.47–19.22 ± 0.13 µg/g DW) was the major phenolic compound. The high antioxidant activity in the fruits of the plant was recorded in the studied RCEs (IC50 = 12.54 ± 0.18–26.33 ± 0.13 μg/ml). A significant correlation between some phytochemical compounds (dependent variable) and morphological features (independent variable) was found. Based on our findings, the fruit of the studied ecotypes can be used for future breeding programs and drug development.