I have the following code:

from sympy import *
init_printing()

x,y = symbols('x y')
u = Function('u')(x,y)
ux,uy,uxx,uxy,uyy = symbols("u_x u_y u_xx u_xy u_yy")

mainEvaluation = uxx - 2*sin(x)*uxy - (cos(x) ** 2) * uyy - 2*ux + (2 - cos(x) + 2*sin(x) )*uy

And when the output of print(mainExpression) is

-2*u_x + u_xx - 2*u_xy*sin(x) + u_y*(2*sin(x) - cos(x) + 2) - u_yy*cos(x)**2

The problem is: I want the original order of variables.

u_xx - 2*u_xy*sin(x)  - u_yy*cos(x)**2  - 2*u_x + u_y*(2*sin(x) - cos(x) + 2)

All this is done in IPython notebook. Is there any way to keep order?

Sadly, SymPy does not keep track of the input order (see the other question I linked in a comment on the question). You can define your own ordering function that orders expressions however you want, but there's no way to order things exactly as they were input, since that information isn't saved.