Due to the low precision and accuracy of trace heavy metals detection wiith traditional energy dispersive X-ray fluorescence (EDXRF) system, an improved EDXRF system is proposed. In order to reduce the influence of reflected rays, the sample is irradiated with the incident X-rays vertically, and the detector is placed in parallel with the sample’s section. The sample is connected with detector through collimator. With improved EDXRF measures certified reference materials, the results show that the detection limit of the improved EDXRF system for Mo，Zn，Cu，Pb，Zr，Nb is 0.4，6.68，1.97，6.84，1.60，7.59 mg·kg-1 respectively and the logarithm deviation of each element in the standard samples is between 0 and 0.05. The RSD%(GBW) is less than 7 as the element content is more than three times of the detection limit, and it is below 15 when the element content is less than three times of the detection limit. The soil samples collected from Da Xing’an Ling region are applied to verify the improved EDXRF system. The proposed EDXRF system can improve the measurement accuracy of trace heavy metal detection in soil, satisfying the requirements of geologic exploration.