The 65 nm-microcontroller units (MCUs) are being widely used in critical terrestrial tests, and the risk from atmospheric neutron becomes more and more serious. The spallation neutron source contains broad energy spectrum, which is different from the mono-energetic neutron sources, and is the most ideal irradiation source for atmospheric neutron single event effect (SEE). Benefiting from China Spallation Neutron Source (CSNS), the atmospheric neutron SEE in 65 nm-MCUs is tested for the first time at the CSNS 9^th beam line in China. The beam line is locatedin the 46° direction along the proton hitting the target, and the neutron spectrum is achieved to range from meV to 1.6 GeV. The test is conducted in two conditions in order to investigate the influence of thermal neutron. One is that the thermal neutrons are shielded with a 2-mm-thick cadmium slat at the beam ejection hole, and the other is not. The detected effects are single bit upset (SBU) events. 16 SBU events are detected when 5.3363 × 10¹⁷ protons hit the tungsten target without the thermal neutron, and 63 SBU events are recorded in the condition of 7.2131 × 10¹⁷ protons striking the target and thermal neutrons included. Comparing with the high energy neutron (>1 MeV), the SBU events caused by thermal neutron contribute about 65% of the number of total upset events. The test results preliminarily illustrate that the thermal neutrons dominate the 65 nm MCU reliability.