An electron beam lithography apparatus comprising an electron lens, a deflector, a reflective electron detector of marks on a stage or a specimen thereon when the deflector scans the marks, and a means for memorizing high order polynomial equations and calculating a correcting value of the deflector controlling means based on the high order polynomial equations, wherein all coefficients of the high order polynomial equation are calculated when the electron beam lithography apparatus starts up, and after then, coefficient of the first order term is calculated from the position signals of the marks frequently in a short cycle.