Based on the fact that rhamnogalacturonan I (RG-I) type pectin gels have good digestive resistance to the stomach and small intestine, which is only degraded to the colon, as well as the good anti-colon cancer effect of nobiletin. In this study, emulsion gel of five different oil phase types (soybean oil, peanut oil, corn oil, sunflower oil and medium chain triglyceride (MCT)) were prepared using RG-I type citrus physiological premature fruit drop pectin (CPDP) as a substrate for in vitro simulated digestion experiments to investigate the delivery effect on nobiletin. The results showed that the bioaccessibility of nobiletin in soybean oil emulsion gel was lower in the small intestine phase relative to emulsion gel prepared with other oils, which was related to the higher saturated fatty acid content of soybean oil and the higher gel strength of soybean oil emulsion gel. Relative to the emulsion, the emulsion gel showed higher retention and lower bioaccessibility of nobiletin in the small intestine phase. Moreover, the centrifugal stability and thermal stability of nobiletin in the emulsion gel were higher than that of the emulsion, and the emulsion gel was stable in the pH range of 2–7 without delamination. In conclusion, the emulsion gel system prepared with RG-I type CPDP may be well suited for the colon targeted delivery of nobiletin, especially when soybean oil is the oil phase, which provides consideration for colon cancer resistance.