High engine speed, but very slow acceleration

Recently, my 2003 manual honda civic accelerates very slowly, even the engine speed goes up to 4000 rpm. Usually it takes up to 1 minute to reach 60mph on high way. Is the clutch getting bad?

That would be my conclusion.
I suggest that you have clutch tested–and replaced if necessary–a.s.a.p., before you wind up stranded somewhere.

It is better to have repairs done on your schedule, and at your mechanic’s shop, rather than at a time and place dictated by sudden mechanical failure.

Extremely likely a worn out clutch.

Typical signs of a worn out clutch.

You need to change the entire assembly; clutch, pressure plate, and throwout bearing. All need doing together.

Sounds like a slipping clutch to me, and that probably means the clutch is worn out.

Better have your mechanic check it ASAP, bacause one day the car won’t move at all.

Thanks so much for all of your suggestions/comments. I will have the clutch checked asap.