The invention discloses a microbial preparation for photovoltaic agriculture and a production method thereof. The microbial preparation is prepared from, by mass, 10%-20% of bacillus subtilis, 10%-20% of streptomyces microflavus, 20%-30% of rhodopseudomonas palustris, 20%-30% of nanometer calcium, 5% of sulfated polysaccharides from brown and 20%-30% of microelements. The raw materials are cultivated to the logarithmic phase in a self liquid medium respectively, the fermentation product is prepared from, by weight, 10%-20% of the bacillus subtilis, 10%-20% of the streptomyces microflavus and 20%-30% of the rhodopseudomonas palustris in a mixed mode, the mixed microbial number is larger than or equal to 2*10<8>, and then the sulfated polysaccharides from brown accounting for 5% of the total mass of the fermentation product, the nanometer calcium accounting for 20% to 30% of the total mass of the fermentation product and the microelements accounting for 20% to 30% of the total mass of the fermentation product are mixed. The microbial preparation is photovoltaic-planting special microbial fertilizer, the problems caused by the novel cultivation mode are solved, and the yield and the quality of plants are improved. As various microelements are added in the microbial preparation, nutrient balance of plants can be met; Fe and Mg have the direct effects on improving the plant chlorophyll content and promoting photosynthesis.