Recent developments in quantum gas microscopy open up the possibility of real-time observation of quantum many-body systems. To understand the dynamics of atoms under such circumstances, we formulate the dynamics under a real-time spatially resolved measurement and show that, in an appropriate limit of weak spatial resolution and strong atom-light coupling, the measurement indistinguishability of particles results in complete suppression of relative positional decoherence. As a consequence, quantum correlation in the multi-particle dynamics persists under a minimally destructive observation. We numerically demonstrate this for ultracold atoms in an optical lattice. Our theoretical framework can be applied to feedback control of quantum many-body systems which may be realized in subwavelength-spacing lattice systems.