In this paper, we demonstrate in situ synchronous frequency comparison between distinct regions in a one-dimensional optical lattice. The synchronous comparison instability is well below the Dick limit and agrees with the limit induced by atomic detection noise. The absolute atom number is extracted from the synchronous comparison instability with an uncertainty below 3%. Surpassing the performance of absorption imaging, this method provides a way to directly and precisely determine the absolute atom number from detection noise. Taking advantage of the inhomogeneous density distribution over the whole lattice, the density shift can also be conveniently measured by this synchronous frequency comparison method. Inconsistent with the expectation of the linear relationship between density shift and atom number difference, nonlinearity is observed, indicating that the assumption of an identical density shift coefficient over the whole lattice is not always safe.