Rishi Sunak, who was only last week appointed the post since serving as an MP for Richmond, posted about his love of the brand in a post on his Twitter account on Friday.
The tweet, which said, "Quick Budget prep break making tea for the team. Nothing like a good Yorkshire brew", prompted a furious backlash from those suggesting it had been sponsored.
The Harrogate-based company has since revealed it has dealt with unnecessarily angry phone calls and messages since Friday, and has asked people to "remember there is a human on the other end".
A series of tweets on the company's Twitter account wrote: "So it's been a rough weekend. On Friday, the Chancellor shared a photo of our tea. Politicians do that sometimes (Jeremy Corbyn did it in 2017).
"We weren't asked or involved - and we said so the same day. Lots of people got angry with us all the same.
"We've spent the last three days answering furious accusations and boycott calls. For some, our tea just being drunk by someone they don't like means it's forever tainted, and they've made sure we know it.
"It's been pretty shocking to see the determination some have had to drag us into a political mudfight. But it's been lovely to see others speak up for us - we're so grateful to everyone who's done that in a civil way (and gutted to see some use it as a reason for more nastiness).
The employee posting the tweets continued: "Speaking directly now, as the person who's been answering these tweets, I know it could have been much worse. It's easier to be on the receiving end of this as a brand than as an individual. There's more emotional distance and I've had a team to support me when it got a bit much.
"But for anyone about to vent their rage online, even to a company - please remember there's a human on the other end of it, and try to be kind."
The Twitter thread on Monday was met with a flurry of responses in support.
Mr Sunak's tweet was shared hundreds of times and received nearly 4,000 replies, many of which accused Yorkshire Tea of political bias.
The Conservative is preparing the Spring budget for March 11.