It also showed that children who are brought up in homes where rules are enforced display strong verbal skills and are more likely to do well in school exams.
The study by the Childhood Wellbeing Research Centre analysed two major surveys of thousands of children.
It looked at the impact of dozens of family factors on children.
Arguing parents and moving to a new school after the age of seven were also found to be stressful events associated with doing badly at school.
The study said: “These findings highlight the continuing significance of family separation, conflict and dissolution on the educational attainment and wellbeing outcomes of young adolescents.”
The research was published by the Department for Education.
The shadow public health minister Diane Abbott recently said family breakdown causes society’s biggest health issues.
She said family units are vital, and doctors have told her broken families cause much of the drug and alcohol abuse they come across.