Motoyama has a humid subtropical climate (Köppen climate classification Cfa) with hot, humid summers and cool winters. There is significant precipitation throughout the year, especially during June and July. The average annual temperature in Motoyama is . The average annual rainfall is with September as the wettest month. The temperatures are highest on average in August, at around , and lowest in January, at around . The highest temperature ever recorded in Motoyama was on 28 July 2007; the coldest temperature ever recorded was on 16 January 2011.
