Brain scans on 12 new mothers soon after birth found more activity in areas linked to motivation and emotions in those who had a vaginal delivery.
The contractions which are an essential part of a natural birth trigger the release of the hormone oxytocin, which is supposed to play a key role in shaping maternal behaviour.
In contrast, similar hormone-triggering does not seem to occur in women undergoing Caesarean.
The procedure has been linked to an increased risk of post-natal depression.
The Yale team carried out brain scans on 12 women two to four weeks after they had given birth - known as the early postpartum period.
Half had a Caesarean, the other half gave birth naturally.
The differences in brain activity were found in regions that not only appeared to influence a mother's response to her child, but also to regulate her mood.
Lead researcher Dr James Swain said the study, reported in the Journal of Child Psychology and Psychiatry, might help provide a better understanding of the chemistry underpinning the attachment between a mother and her baby.
"Our results support the theory that variations in delivery conditions such as with caesarean section, which alters the neurohormonal experiences of childbirth, might decrease the responsiveness of the human maternal brain in the early postpartum."
Professor James Walker, a spokesman for the Royal College of Obstetricians and Gynaecologists, said: "We have long recognised that people who have a caesarean section do sometimes have some problems bonding with their baby."
However, Professor Walker said the reason for this was unclear. In some instances, it might be related to clinical difficulties which made a caesarean necessary in the first place.
The latest study selected only women who opted for an elective Caesarean alongside the six who gave birth naturally, but Professor Walker said there might be specific personality characteristics within the former group which made maternal bonding more difficult.
He said it was also possible that women who had a Caesarean were slightly disengaged from the birth process in comparison to those who went through a natural delivery, BBC reports.
Professor Walker said there were no long-term studies assessing whether mothers who had a Caesarean had longer-term problems bonding their baby.
"There is no doubt that many women who have a Caesarean turn out to be wonderful mothers," he said.
Belinda Phipps, of the National Childbirth Trust, said: "Bonding between a mother and baby is highly important and responding to a new baby's cry is a key part of maternal attachment.
"Women who have a Caesarean section should be encouraged to cuddle their newborn against their skin straight after birth and be offered practical support to help them fed and care for their baby."
Between 10% and 20% of all births in the UK are now delivered by Caesarean.
There is concern that too many women opt for an elective Caesarean, a major surgical procedure, with a risk of side effects.