Hi. Is there any way to invert axis from y to x cause that what happened on my cnc router. My short axle is  x but is should be y. Because of that every project i send to cnc have to be rotated by 90 degrees. Where should i look for fault.

Not sure I fully understand but it seems from what you are saying you want to swap the x and y axes.  If that is the case then co to config->ports and pins, select the motor outputs tab and swap the pins settings for the step and dir pins.  Or, just swap the cables for the x and motors ;^)