Authorities said the security threat had eased, and the “intensified efforts” at Denmark's land border with Germany were being scrapped on the advice of domestic intelligence.
Police had set up temporary border posts at what is usually an open border in Europe's Schengen zone, leading to queues at road crossings.
The checks were brought in on August 4 amid fears of reprisals against Denmark and Sweden, after several protests where the Quran was desecrated.
The acts led to condemnation and counter-protests in the Muslim world. Danish intelligence said it was aware of calls for reprisals by Al Qaeda.
Danish border guards were told to check whether people had “legitimate business” in the country.
Sweden has similarly tightened rules.
However, the Danish intelligence assessment is that “the current security situation in Denmark is not considered to require the maintenance” of additional checks, the government said.
As a result there will be no permanent staffing at the road crossings and police resources will be diverted to “strengthening crime-fighting efforts in the border areas”.
Sweden, in contrast, last week raised its terrorist threat level from “elevated” to “high” in the wake of the Quran burnings.
Both countries are considering whether to tweak the free expression laws that allow the protests to go ahead with police approval.
The Swedish government's stance that police only approve gatherings, and not the Quran-burnings that may take place there, has failed to repair damaged relations with Muslim countries.
A Swedish review will consider whether police can intervene when there is a security threat falling short of war – the only circumstance in which authorities can currently step in.
However, some political parties in both Sweden and Denmark have come out against a change in the law.
A Swedish police attempt to block further protests, after the Quran was burnt outside Turkey's embassy in Stockholm in January, was blocked by a court on free speech grounds.
Ministers have said they do not approve of burning the Quran.
The EU says such acts are not compatible with its values but that it is up to member states to decide whether to ban them.