What does Matthew 12:41 mean?

Jesus has declared that this generation, His generation, is evil and spiritually unfaithful to God. The only sign they will receive from God to validate that He is the messiah is what Jesus as called "the sign of Jonah." As Jonah was in the great fish for three days and nights, Jesus, the Son of Man, will be in the heart of the earth for three days and nights (Matthew 12:39–40). This is a prophecy about Christ's death and resurrection, however difficult that would have been to understand before it happened (John 2:19–22).

Earlier, Jesus referred to a day when all people would face judgment by God (Matthew 12:36). This statement might not mean that everyone will literally see the judgment of all other people. Jesus' greater point in referring to Nineveh is that those people—wicked as they were—properly responded to the preaching of Jonah. On that day of judgment, the people of Nineveh will righteously criticize the generation of Israelites who lived at the time of Jesus. When the people of Nineveh heard about God's coming judgment, they repented of their great evil, from the king down. They turned from their sin and began to pray to God.

The generation of Israelites during the time of Jesus, however, had not repented. They did not turn from their sin, including the sin of not believing Jesus to be the Messiah. This was despite Jesus, as the Messiah, being far greater than the reluctant prophet Jonah.

Proud Pharisees and other faithful Jews would have been stung to hear this. The reason Jonah was so reluctant to go to Nineveh was probably anger over the terrible things that culture had done to his own Jewish people. It would have been painful for an ancient Israelite to be condemned by formerly wicked, antagonistic Gentiles. The key difference between the two groups was repentance—so those who ignore Christ's message have no excuse.