The invention provides a physical package based on an MEMS (Micro-Electro-Mechanical System) atom chip and a packaging method thereof, and relates to a physical package and a packaging method thereof. The invention solves the problems of excessive heating power consumption and magnetic interferences in the application process of the existing miniature alkali metal atomic steam chamber in a sensor system. The package is as follows: a ceramic shell is respectively hermetically connected with an upper light transmitting window and a lower light transmitting window; an upper support membrane and a lower support membrane are bonded to the upper and lower surfaces of the micro-structure atomic chip; the micro-structure atomic chip is connected with an inner connecting bracket; and the upper support membrane and the lower support membrane are bonded to a base of the ceramic shell inside a package cavity. The method comprises the following steps: sealing the lower light transmitting window and the sealed ceramic shell; bonding the upper support membrane and the lower support membrane on the micro-structure atomic chip; fixedly connecting the upper support membrane and the lower support membrane; fixedly connecting the micro-structure atomic chip and the inner connecting bracket; connecting heating and thermoscope leads of the upper support membrane and the lower support membrane to an inner electrode; and connecting the inner electrode to an outer electrode. The invention is applied to the field of micro-electro-mechanical systems.