The invention provides a compound microorganism profile control bacterium agent as well as a preparation method and application thereof. The compound microorganism profile control bacterium agent is prepared from the following components in percentage by mass: 5 percent to 10 percent of a microorganism profile control bacterium agent, 0.2 percent to 0.3 percent of corn grains, 0.2 percent to 0.5 percent of a high molecular polymer, 0 to 0.2 percent of an auxiliary agent and the balance of water, wherein the microorganism profile control bacterium agent is fermentation liquid obtained by fermentation culture on lasiodiplodia theobromae for profile control with the preservation register number of CFCC 85199 in an optimized PDA culture medium; the compound microorganism profile control bacterium agent contains rich mycelial fungi and polysaccharide metabolites which are naturally formed in a microorganism growing and propagating process; when being applied to a low-permeation non-crack oil reservoir, the compound microorganism profile control bacterium agent can enter a deep part of the low-permeation oil reservoir under a suspension effect of the high molecular polymer; growth and propagation are carried out by utilizing a slow-release nutrient component, namely the corn grains, and the auxiliary agent, or the corn grains are used as carriers for growth in an attachment manner; pore permeation type high-permeation belts, micro-cracks and the like are effectively blocked; the compound microorganism profile control bacterium agent is low in injection viscosity, good in injection property, simple in process and safe to construct.