When you print os.path.isfile(i), you’re checking if “1.txt” or “2” or “3.txt” is a file, whereas when you run os.path.isfile("/home/user/Desktop/1/1.txt") you have a full path to the file.
Try replacing that line with
print(os.path.isfile("/home/user/desktop/1/" + i))
Edit:
As mentioned in the comment below by icktoofay, a better solution might be to replace the line with
print(os.path.isfile(os.path.join("/home/user/desktop/1", i)))
or to earlier store “/home/user/desktop/1” to some variable x, allowing the line to be replaced with
print(os.path.isfile(os.path.join(x,i)))