That they are entirely different language families. Japanese is more or less a language isolate belonging to the somewhat mysterious "Japonic" family which is attested first in the 6th century CE. It may be related to Korean and have some now extinct Korean varieties, and may be more broadly relates to a hypothetical Turko-Mongolian family (unlikely the family itself is highly contraversial), Austronesian languages (slightly more likely), or Austroasiatic (again, very unlikely). Chinese, or rather the Sinitic language family, are part of the Sino-Tibeto-Burman family. The language group broke off from Tibeto-Burman between 3000BCE and 1200BCE, probably closer to the later, and moved North or Northwest from the Urheimat to the Yellow River Valley and established there, expanding outwards between 1200 and 500 BCE where a stark linguistic divide appears and develops into several distinct languages throughout modern China.

Chinese had had a strong influence on Japanese due to sustained contact during the establishment of Japanese kingdoms. Cognates are thus found in Japanese language. The writing system was adopted by the Japanese and modifications were made over time. Modern Japanese uses three scripts based on Chinese: Kanji, which is largely Chinese character with a few different pronouciations; Hiragana, which is a pjonetic system developed by court women in Heian Japan; and Katakana, a system used for foreign words and names.

Written Chinese and Kanji had a few differences, but during the Republican period, written Chinese adopted simplified characters to improve literacy in rural China, leading to a much greater divergence.