The lengthy article is the latest move in an escalating war of words that have stoked tensions on the Korean peninsula.
On Monday the US state department expressed concern over the increasing hostility between the two Koreas, saying the harsh rhetoric was not helping the much-delayed six-nation nuclear disarmament talks.
Christopher Hill, the US chief nuclear negotiator, was due to arrive in Seoul later on Tuesday to discuss ways to restart the stalled talks amid signs of growing impatience by the two Koreas.
In its commentary the Rodong Sinmun described Lee's policy toward the North as a "declaration of war", warning that the new president was "making a mess of the process to denuclearise the peninsula".
February 25 Lee Myung-bak takes office as South Korean president. Promises to end unconditional aid to North, saying Pyongyang must improve human rights and return Southerners held since the 1950-53 Korean War
March 26 South Korean military chief tells MPs military will strike suspected nuclear weapons site in North if Pyongyang attempts to attack South with atomic bombs
South Korean foreign ministry says it will back a UN resolution condemning North's human rights record, ending a decade of reluctance by previous administrations
March 27 Pyongyang expels South Koreans working at joint industrial zone in the North
March 28 North Korea test-fires missiles into sea and warns it will "mercilessly wipe out" any South Korean warships that violate its waters
March 29 North warns inter-Korean reconciliation may be in jeopardy, implements ban on South Korean officials entering the country
March 31 North Korea threatens to turn the South to "ashes" after South's warning of pre-emptive strike in response to nuclear attack
April 1 North accuses South Korean president of being US stooge and causing instability on peninsula
Timeline: The Two Koreas
"Lee's seizure of power created a thorn bush in the way of the inter-Korean relations", it said, warning against misjudging "the patience and silence so far kept by" the North.
Aside from the barbed rhetoric recent days have also seen Pyongyang test-firing missiles, ejecting South Korean officials from a shared industrial zone and accusing South Korean ships of breaching a disputed sea border last week.
On Sunday the North threatened to turn its neighbour to "ashes" after South Korea's military chief said he would consider of a pre-emptive strike if the military believed North Korea was preparing a nuclear attack.
Lee, who pledged a tougher line on ties with the North, has said that South Korean aid to the impoverished North will no longer be given unconditionally.
In a marked change from previous administrations he has also warned that his government will not shy from criticising Pyongyang's human rights abuses.
Lee's conservative Grand National Party, responding late on Monday to the "ashes" threat, called on the North to stop "blackmailing" the South.
"We should face North Korea's military threat dauntlessly and resolutely," the party said in a statement.
Last year North Korea last year signed a pact agreeing to disable its main atomic plants and declare all its nuclear programmes and materials by the end of 2007.
But the process has become bogged down over a US demand that North Korea supply a full and accurate declaration of its nuclear activities, including its alleged proliferation of nuclear technology to third countries.
According to a report in South Korea's Chosun Ilbo newspaper on Tuesday, the chief US nuclear negotiator recently confronted North Korean officials with US evidence of North Korea's alleged nuclear links with Syria.
The newspaper said Hill presented Kim Kye-gwan, the North's nuclear envoy, with a list of officials and engineers said to be involved in the technology transfer, but did not say where the meeting took place.
The North's purported connection with Syria is among the key issues holding up progress in the denuclearisation deal.
The US embassy said Hill would hold two days of talks in South Korea until leaving for Indonesia on Thursday.