The invention discloses an erigeron breviscapus root rot control agent and an application thereof, and belongs to the technical field of pesticides. The control agent provided by the invention is prepared from the following components by weight: 1-2 parts of copper sulfate, 1-2 parts of quick lime and 3,000-9,000 parts of floating seedling pool water. Before erigeron breviscapus germinates or after seedlings of erigeron breviscapus sprout, the control agent provided by the invention is added in a floating seedling pool to immerse root systems of erigeron breviscapus, so that infections of fusaria can be effectively suppressed. The control agent has an obvious effect for inhibiting propagation of blue-green algae, retains breathability of a seed bed, has a very good control effect for root system diseases, can effectively control the length of the erigeron breviscapus root systems, and controls the length of the root system within 3-4 cm and at a relatively ideal state.