I have Honda CB Trigger 150cc 14BHP@8500 & 12.5NM@6500. Whenever I ride in higher altitudes (above 3000m), Its power decreases gradually.
Is there a way to increase the low end torque without doing major external modifications?
It is struggling in the thinner atmosphere as your height increases. You need to increase the amount of air going into the engine to have any chance or get a larger bike with more low end torque that won't notice the losses so much.
Edit to reply to comment about changing rear sprocket for a larger one. Yes, you can do this, but you limit the top end speed at the same time - this means that if you hit max engine rpm going downhill before changing the sprocket then you will be running the engine at max rpm for longer after changing it and decreasing the engine life quite substantially.
Though you have a small engine, and the difference will be minimal, but increasing intake manifold runner length will move torque curve lower in the RPM range. But this will affect peak torque figures, as well as engine revving character - it will not be as rev-happy.
There's less air pressure the higher you go. By the time you get to 3000m, you have about 2/3 of what there is at sea level. It gets worse the higher you go. Bikes with carburetors tend to lose more power with altitude, since the fuel/air mixture generally goes rich when you get into high elevations. I suppose you could add a turbocharger to increase manifold density at high altitude, but that would be rather involved. The simplest fix is to simply buy a more powerful bike. For example, my current bike has 105 hp at sea level. At the higher mountain passes where I ride, it's down to about 65. That's still a lot more than my old bike that had 36 at sea level.