When X-ray fluorescence (XRF) is used in analyzing the element composition of the sample in air atmosphere, the strong absorption from the air to the low-energy characteristic X-rays from such low atomic number (Z) elements as Cl, K, Ca, and so on, deeply affect the analysis for them.To avoid the strong absorption from the air to the characteristic X-ray of low Z elements, the XRF technology in a vacuum atmosphere is often used, but it requires a complicated and expensive vacuum system. Besides, the power of the laboratory source is generally low. This results in a low intensity of incident X-rays, which also affects the analysis of the element composition of the sample with XRF. To solve the above problems, a simple closed XRF analysis system in a helium atmosphere based on a monolithic polycapillary X-ray lens (PCXRL) and rotating target X-ray source was designed. Strong XRF signals were obtained by using X-rays with a high gain of power in density focused by the PCXRL to irradiate the sample, and the excitation channel and the detection channel were both in a stable helium atmosphere to reduce the absorption from the air to the characteristic X-rays of low Z elements. The designed XRF system was characterized to show that with a rotating molybdenum target working at a voltage of 29 kV and a current of 20 mA, the detected XRF intensity of Cl, K, Ca, and Fe in a helium atmosphere is higher than that in an air atmosphere, respectively. For elements with an energy of the characteristic XRF below 8 keV in plants, the characteristic XRF intensity detected in the helium atmosphere is 1.1 to 5.5 times that in the air. This is helpful for an efficient and non-destructive XRF analysis of the elements with low Z of samples.