I have a line in three dimensional space starting from origin and end point is also known parameter.The line is rotating in 3D with origin as (0,0,0).How can we find the new end position by rotating angle and initial start and end position of line ?

Since you are at the origin, the vector itself will give you the end point.

So if your vector is 3,3,3 then the end point is 3,3,3. Rotate it in whatever circumstances and the vector (x,y,z) is now the point at the end of it.