The miniature Neutron Source Reactor (MNSR) is manufactured by the Chinese Institute of Atomic Energy, It is a low power, tank-in-pool type research reactor and similar to the Canadian SLOWPOKE Reactor, The reactor employs highly enriched uranium as fule (90.2%), light water as moderator and coolant, and metal beryllium as reflector. Heat generated in the core is removed through natural convection. In this work, the Isfahan Miniature Neutron Source Reactor (MNSR ) has been simulated using the MCNP Code, and reactivity worth of flooding the inner irradiation sites of this reactor in an accident hasbeen calculated. Also, by putting polyetilen capsuls containing water inside the inner irradiation sites, reactivity changes of this reactor in such an accident have been measured, the results of which are in good agreements, with the calculated results. In this work, the reactivity worth due to flooding one inner irradiation site is about 0 .53mk , and reactivity worth due to flooding of the whole 5 inner irradiation sites is estimated to be about 2.5 mk. Key words MCNP Code, Monte Carlo Simulation, Reactivity, MNSR Reactor