In the process of quantitative analysis of low content of Cu and Mo in molybdenum-copper ore by energy dispersive X-ray fluorescence spectrometry, the original spectrum of X-ray tube has a great influence on the measurement results. In order to reduce this effect, Monte Carlo software was used to simulate the influence of filters of Ag, Cu+Mo and Ti on the original spectrum under different thickness conditions. The simulation results showed that the effect of measuring copper and molybdenum elements with 1mmTi filter is better than that of 0. 2mm Ag filter, which is better than the case of using 0.02 mm Cu and 0.1 mm Mo as filters. According to the simulation results, the thickness of the three kinds of filters was measured. By comparing atlas of spectrolines showed that When Cu+Mo is used as a filter to measure molybdenum, the background count is greater than 200, and when using Ag and Ti as a filter, the molybdenum element is measured, and there is almost no background influence. However, for the same sample, the highest count of molybdenum was about 800 when Ti was used as the filter, and the highest count of molybdenum was about 300 when using Ag as the filter. It can be seen that when the molybdenum element is measured by using Ti as a filter, the original spectrum of the X-ray tube has little influence on the interference of the measuring element, and the background thereof is lower than that of the silver filter and the copper-molybdenum filter. The Ti filter has the highest count rate of molybdenum while reducing the background effect, indicating that the ray strength loss is the least. When Cu+Mo is used as a filter to measure copper, the highest count of copper is 300. When using Ag as a filter, the highest count of copper is about 180, while the highest count of copper using the filter is about 500. It can be seen that when the content of copper is low, the use of Ti as a filter to measure copper elements has the highest count rate of copper and the least loss of ray strength. The calculation by formula showed that the detection limit of copper in molybdenum-copper ore is 5.63 mg·kg-1 with 1 mm Ti filter, and the detection limit of molybdenum is 1.39 mg·kg-1, and the detection limit is significantly reduced. Using different standard samples for measurement andchemical analysis fitting, the working curve shows that the high and low content samples have a good linear relationship, the error level meets the normal chemical analysis error standard, R2 is 0.99 and above, indicating that 1 mm Ti is passed. The measurement results by using 1 mm Ti filter are highly Precision. Selecting any one of the production samples for repeated measurements, the RSD (%) of the Cu element is 0.59, and the RSD (%) of the Mo element is 0.3, which is less than 1, indicating that the instrument has good measurement stability and the sample test results are reproducible. In this paper, the determination of molybdenum and copper in molybdenum copperore by energy dispersive X-ray fluorescence spectrometry, Monte Carlo simulation analysis provides a credible basis for the selection of filters and the determination of their thickness. A 1 mm Ti filter was selected and tested on-site. The method is stable and reliable and has important practical application value.