Camellia oleifera is a major woody oilseed species in China, but it is typically cultivated in nutrient-poor soils and may be affected by various trace elements. This study examined how spraying selenium, boron, and zinc trace elements affected the traits and functional active compounds of C. oleifera under nutrient deficiency. The results revealed significant variations in the effects of different trace element combinations on C. oleifera. Optimal concentrations of zinc and selenium are critical for promoting the growth and development of C. oleifera fruit. The transverse diameter of the fruit, the single fruit weight, the number of seeds per fruit, the single fresh seed weight, the oil content in the fruit, and the oil yield per plant of other treatments can be increased by up to 3.07%, 10.57%, 23.66%, 30.23%, 7.94%, and 21.95%, respectively, at most, compared to the control group. Diluting zinc from 1000 to 1500 times and maintaining a selenium concentration from 100 to 200 mg/L has been found to be beneficial for fruit growth. While low concentrations of selenium may promote an increase in fruit transverse diameter, high concentrations of selenium, along with high dilutions of zinc, can have the opposite effect, leading to a reduction in fruit diameter. However, a high concentration of selenium can positively impact the number of seeds per fruit. The most effective combination was found to be a selenium concentration of 0 mg/L, a boron concentration of 4 mg/L, and a zinc dilution of 1500. Interestingly, lower concentrations of selenium and boron, as well as lower dilutions of zinc, were found to increase the oil yield per plant. This suggests that a careful balance of trace elements is required to promote both fruit growth and oil content. The total sterol, squalene, total flavonoid, and polyphenol content of other treatments can be increased by up to 28.81%, 32.07%, 188.04%, and 92.61%, respectively, at most, compared to the control group. Selenium fertilizer and boron fertilizer increased the total sterol content in Camellia oil and had a significant positive correlation at the 0.01 level, but zinc fertilizer had little influence on it. High concentration selenium fertilizer generally increased the squalene, total flavonoid, and polyphenol content in Camellia oil, but boron and zinc fertilizers had little effect on these components. The results suggested that choosing appropriate fertilizer combinations could improve nutrient deficiency in C. oleifera and enhance the functional active compounds of its oil, thereby enhancing its value.