The invention provides a method for matching the particle size of elastic microspheres used for profile controlling and flooding of an oil reservoir deep part with a pore throat. The method includes the steps that an oil reservoir pore throat diameter distribution parameter is obtained; according to the diameter of the pore throat, a diameter-variable pipe with the diameter same as that of the pore throat, and the breakthrough pressure and deformation migration ability of the elastic microspheres with a certain initial particle size in the diameter-variable pipe under the different-expanded-ratio conditions are measured; through a nuclepore membrane experiment, the filtering time and filtering volume of the elastic microspheres with a certain particle size are obtained after the elastic microspheres pass through nuclepore membranes different in pore diameter; a filtering-time and filtering-volume curve is drawn, and the matching range of the particle size of the microspheres obtained by the deformation migration of the elastic microspheres into one nuclepore membrane with the diameter of the pore throat, the elastic microspheres with corresponding particle size are selected, and profile controlling and flooding of deep part is designed and implemented. According to the method for matching the particle size of the elastic microspheres used for profile controlling and flooding of the oil reservoir deep part with the pore throat, by effectively blocking off the oil reservoir pore throat, the expansion of the water flooding sweep range is achieved, the temperature resistance, salt tolerance and block-off effects are good, the block-off effect of the deformation migration of the elastic microspheres are given play to, and no damage is caused to a reservoir.