Why didn't mendeleev use atomic number to arrange the elements?

The primary reason for this was that Mendeleev didn't know that atomic numbers actually existed. Atomic numbers were only discovered a period after Mendeleev's time. The use of X-rays made it possible to find the atomic number, and those had not been discovered yet. 
The periodic table was then arranged in 1913 by Henry Moseley in an arrangement according to atomic number.