In a series of tweets posted hours after the test, Trump denounced the North but also criticised Seoul.
More than 24 hours after Pyongyang shook the ground and the world with what it said was a hydrogen bomb test, the US president had yet to speak to his South Korean counterpart Moon Jae-In.
But he had already had a telephone conversation with Japanese Prime Minister Shinzo Abe, their second of the weekend.
In a series of tweets posted hours after the test, Trump denounced the North but also criticised Seoul, saying: "South Korea is finding, as I have told them, that their talk of appeasement with North Korea will not work, they only understand one thing!"
That came after he said on Saturday he was considering pulling the United States out of its free trade pact with the South -- an economic deal that analysts say underpins the breadth of the relationship between the two countries, which have been security allies for nearly 70 years.
Trump's unexpected attack on the country took many by surprise, and analysts say his undisciplined tweets were worsening the situation at a crisis moment.
Moon backs engagement with the North as well as sanctions to bring it to the negotiating table, and called for stronger measures in response to the latest nuclear test.
But John Delury of Yonsei University in Seoul said Trump was comparing Moon to Neville Chamberlain, the British prime minister who sought to satisfy Adolf Hitler's territorial demands in Europe before the Second World War.
"What it indicates is that he puts so little value in that relationship right now that he is willing to publicly attack his partner in Seoul," he told AFP.
The US is security guarantor for the democratic and capitalist South, where 28,500 US troops are stationed to defend it from Pyongyang after the 1950-53 Korean War ended with a ceasefire instead of a peace treaty.
The alliance with Seoul has been a key pillar of Washington's geopolitical strategy in Asia, where China is increasingly flexing its muscles and the North has made rapid advances in its weapons programmes.
But as well as talking to Japan's Abe, Trump tweeted that China was "trying to help but with little success".
"The hierarchy is clear that South Korea is at the bottom of the pile," Delury told AFP.
Trump's approach could be "absolutely fatal for US NK policy" tweeted Adam Mount, senior fellow at the Center for American Progress, adding: "Alliance cohesion is the easiest and most important signal to send today."
"Trump's views on trade, negotiations, policy inconsistency, threats, & other slights have ravaged the alliance," he said.
-- 'Dumb and dangerous' --
On the campaign trail, Trump accused South Korea of not paying enough for its defence and threatened to scrap a "horrible" bilateral trade pact, triggering major concerns about the alliance.
Those concerns have resurfaced in Seoul after Trump said that he would discuss the possible withdrawal from the five-year-old US-Korea free trade agreement (FTA), known as KORUS, with his aides this week. "It's very much on my mind," he said.
The trade pact carries symbolic value as it had been billed as something that can "buttress the alliance", said Delury.
Scrapping it would be the economic equivalent of "pulling the rug out" from underneath South Korea just when it is under threat from the North, Delury said.
South Korean media also warned of the potential consequences.
Terminating the deal would "send the wrong message to North Korea about the alliance", the JoongAng Ilbo said in an editorial Monday, "at a time when North Korea has pushed brinkmanship over nuclear and missile programs to the limit".
Colin Kahl of Georgetown University, who worked for the Obama administration, said the US should make reassuring South Korea and Japan its top priority.
"Undermining alliance solidarity at this moment is dumb and dangerous," he tweeted, adding: "The Administration needs to speak with one voice before confusion splits the US from its allies, produces a war, or both."