The methodology to treat the infection of XXX mostly use chemical pesticides, which is less effective and not eco-friendly, as well as it produces a residue.
Is "not eco-friendly" a negative form?
Yes, technically speaking, not eco-friendly is the negative form of eco-friendly. This is just like saying that the negative form of a good man is not a good man. Simple as that. But the closest thing I can think of that can be considered a more interesting negative form for eco-friendly is:
detrimental to the environment
As many people have already pointed out, your original sentence does sound slightly awkward. So, I changed the wording a little bit:
The most common method used to prevent plant diseases today is use of pesticides which in reality are not even that effective and can actually be very detrimental to the environment. They also leave residual deposits which remain in the ground for years.
Also, check out the suggestions offered by CopperKettle in the comments section.
"eco-unfriendly" would be the opposite of "eco-friendly".
"Not eco-friendly" could mean either "eco-unfriendly" or "eco-neutral".