Trump condemned the inquiry in a tweet as "without due process or fairness or any legal rights", the BBC reported.
But Democrats were outraged at the President for invoking such a grim and racist chapter from US history.
Lynching refers to historic extrajudicial executions by white mobs, mainly against black people.
White House spokesman Hogan Gidley told reporters on Tuesday that Trump did not mean to be racially insensitive.
"The president has used many words, all types of language, to talk about the way the media has treated him," the Deputy Press Secretary said.
He added: "The President wasn't trying to compare himself to the horrific history in this country at all."
The impeachment inquiry is examining whether the Republican President abused his office by improperly pressuring Ukraine to launch an investigation into former US Vice-President Joe Biden, a leading candidate for the Democratic 2020 presidential nomination.
Trump denies holding up US military aid to Ukraine so they would investigate Biden's son, who worked for a Ukrainian gas company.
Trump has repeatedly called the impeachment inquiry, as well as an earlier investigation into foreign meddling in the 2016 election, a "witch hunt".
But his likening of a process enshrined in the US constitution to racist killings provoked outrage among African-American lawmakers.
( With inputs from IANS )