Both of the home side's goals came courtesy of contentious decisions from the official, with a soft penalty allowing Mark Noble to open the scoring in the third minute, before Joey O'Brien scored the winner despite Norwich's Alexander Tettey laying prone with a head injury.
Clattenburg also waved away two penalty appeals from Norwich - one a definite handball and the other a debatable collision - as the visitors fell to their fourth defeat in a row.
Hughton accepted his team were under par, but was nevertheless unhappy with Clattenburg.
"It's been very harsh on us with the decisions today," he said. "The major decisions went in West Ham's favour - and it's difficult to take that.
"We have been harshly treated. If you are going to give a penalty so early in the game, that's his [Clattenburg's] prerogative, but when you also have two shouts for penalties, [it's tough to accept]."
West Ham's penalty was awarded for a pull on Winston Reid by Ryan Bennett.
Hughton conceded that Bennett had hold of the West Ham defender's shirt, but insisted his man was also being fouled.
"I accept that Ryan Bennett has got hold of his shirt, but they are very close together and Reid has got his elbow in Bennett's neck," he added.
"I will accept that Ryan has got hold of Reid's shirt, but it's not like he was pulling him away. If anything, Reid is impeding him. It was a little bit of each. That is my big argument."
The second goal came after Tettey went down following a clash that kept him grounded for several minutes.
Hughton said there was no question that play should have been stopped.
He said: "Alex Tettey gets pole-axed in the middle of the park. I can't see any referee anywhere not giving that."