Pilot fatigue and alertness are critical for civil aviation safety. Intercontinental pilots are more prone to fatigue and sleepiness due to jet lag, prolonged workdays, and disrupted rhythms. The Civil Aviation Administration of China excused enlarged flight crews from mandatory layovers and reimposed flight duration restrictions during COVID-19. This study investigates the sleep quality and attentional performance of pilots on intercontinental flights. The fifteen pilots who performed intercontinental flights in different crew compositions wore a body movement recorder, which has been proven to accurately estimate sleep duration and sleep efficiency. The crew’s attentional performance and self-report were monitored at specified flight phases. In conclusion, the larger crews slept longer and more efficiently on board, particularly pilots in charge of takeoff and landing responsibilities. Crews on four-pilot layover flights were more alert before the takeoff of the inbound flights than exempt flights, but there was no significant difference towards the end of the mission. The new long-haul flight organization did not result in fatigue or decreased attention in the pilots. This study expands on the research by validating a novel intercontinental flight operation model under the COVID-19 scenario and highlighting critical spots for future fatigue management in various crew compositions.