We propose a method that enables precise determination of the number of atoms in a Dick-noise-free optical lattice clock, by effectively addressing quantum projection noise. Our approach relies on conducting stability measurements at three distinct parameter sets, allowing us to differentiate between quantum projection noise, photon shot noise, and technical noise. Importantly, our method enables accurate extraction of the atom number, even in the presence of photon shot noise and technical noise. To validate the effectiveness of our approach, we employ numerical simulations and optimize the modulation parameters to achieve the smallest uncertainty possible. The numerical simulations show the validity of our method and demonstrate a measurement uncertainty in the atom number that is below 4% across a wide range of atom numbers, provided that the standard deviation of atom number fluctuation is kept below 0.23 times the average atom number.