"This injury outweighs any interest the state might have in banning abortions after the detection of a foetal heartbeat," he said. The law was set to go into effect on July 1.
Reeves had reportedly expressed anger and frustration during a court hearing on the law earlier this week. He was upset over the rule not including exemptions for rape or incest.
The judge pointed out that he struck down a 15-week ban on abortion just six months ago, saying the state legislature's even stricter law "smacks of defiance", the Washington Post reported.
Reeves issued his ruling amid a national furore over strict abortion laws.
The legislation, also known as a "heartbeat bill," prohibits abortions after an ultrasound can detect electric activity from what will become a foetus' heart, a milestone that could come just six weeks into a pregnancy. The bill sped through the statehouse and Mississippi Governor Phil Bryant signed it in March.
It is now the second six-week ban to be passed and blocked this year. In March, a federal judge in Kentucky halted a similar six-week measure, questioning the law's constitutionality.
In a statement, Bryant said he was disappointed with the decision and indicated he would direct his attorney general to review it.
Alabama became the subject of national headlines earlier this month after lawmakers there passed the strictest abortion law in the country, effectively blocking the procedures altogether.
Nancy Northup, President of the Centre for Reproductive Rights, which filed the lawsuit, said: "The Constitution protects a woman's right to make decisions over her body and her life. The district court's decision today was a resounding affirmation of this settled law."