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Although the sun is really far away from us, some solar activities could still influence the performance and reliability of space-borne and ground-based technological systems on Earth. Those time-varying conditions in space caused by the sun are also called space weather, as the atmospheric conditions that can affect weather on the ground. It is known that aviation activities can be affected during space weather events, but the exact effects of space weather on aviation are still unclear. Especially how the flight delays, the top topic concerned by most people, will be affected by space weather has never been thoroughly researched. By analyzing huge amount of flight data (~5X106 records), for the first time, we demonstrate that space weather events could have systematically modulating effects on flight delays. The average arrival delay time and 30-minute delay rate during space weather events are significantly increased by 81.34% and 21.45% respectively compared to those during quiet periods. The evident negative correlation between the yearly flight regularity rate and the yearly mean total sunspot number during 22 years also confirms such delay effects. Further studies indicate that the interference in communication and navigation caused by geomagnetic field fluctuations and ionospheric disturbances associated with the space weather events will increase the flight delay time and delay rate. These results expand the traditional field of space weather research and could also provide us with brand new views for improving the flight delay predications., Comment: submitted to science advances