A woman's overall health during pregnancy also has an impact on the health of the child in later life, the report said.
Dame Sally said she wanted to "bust the myth" that women should eat for two when pregnant, adding a healthy diet with fruit and vegetables and avoiding alcohol was important.
Prof Nick Finer, from University College London's Institute of Cardiovascular Science, said obesity was now "the most pressing health issue for the nation".
"Estimates of the economic costs of obesity suggest they will bankrupt the NHS.
"Elevating the problem of obesity to a national risk could help to address the current 'laissez faire' attitude to this huge, angry, growing health catastrophe," he said.
In her report, Dame Sally highlighted the need for early diagnosis and treatment of eating disorders, such as anorexia, bulimia and binge-eating, which are more common in women than men.
She recommended that everyone with an eating disorder should have access to a new and enhanced form of psychological therapy, available online, called CBT-E, which is specifically designed to treat any eating disorder.
This should be available to all age groups across the country, she said.
Lorna Garner, from Beat, the charity that supports people with eating disorders, said the recommendation would have "a dramatic and positive impact on a very large proportion of the individuals diagnosed with eating disorders".
The report also called for better treatment for ovarian cancer, which kills more women in England than any other gynaecological cancer.
With survival from the cancer among the lowest among developed nations, Dame Sally recommends longer operating times to increase the likelihood that all the cancer is removed during surgery.
Training in specialised surgical skills to remove gynaecological cancers and an audit of treatments are also highlighted in the report.
There should be more awareness of women's problems "below the waist" and more discussion of taboo topics such as urinary and faecal incontinence and the menopause, the report said.
More than five million women suffer from incontinence in the UK, a condition that can seriously affect the quality of their lives.
Bosses should also make it easier for women to discuss their menopausal symptoms without embarrassment, which could help them reduce their sick leave and improve their wellbeing at work.
Elsewhere in the report, the chief medical officer recommended that:
clinical staff be better trained to recognise and respond to violence against women, including female genital mutilation, domestic abuse and sexual violence
more research is needed to improve maternal and child mental and physical health
more research on screening tests, preeclampsia and foetal growth is also needed
children should receive integrated personal, social, health and economic education (PSHE) with sex and relationships education (SRE) at school
a full range of contraception services should be available to all women, at all reproductive ages
Dr David Richmond, president of the Royal College of Obstetricians and Gynaecologists, said women should be placed at the centre of their care throughout their lives.
He said issues such as maternal obesity, poor diet, lack of physical activity, high levels of alcohol consumption, smoking and poor sexual health "must be addressed... to enable all women to make safe and appropriate lifestyle choices".