The invention discloses an online monitoring system of pollen in atmosphere. The online monitoring system comprises an impact-type sampler, an optical microscope, a sampling membrane band, a conveying rotating shaft, a pneumatic control valve, a CCD camera, a sampling pump and an industrial personal computer. The impact-type sampler is connected with the atmospheric environment. The sampling pump is connected with the impact-type sampler through a connecting pipe, exhausts air from an outer sampling pipe of the impact-type sampler, and is used for collecting pollen particles in the atmosphere on the sampling membrane band. The sampling membrane band is controlled by a system to be conveyed to the portion below the optical microscope for observation and analysis. The CCD camera is used for collecting pollen sample image information and transmitting the pollen sample image information to the computer for image analysis. The online monitoring system is simple in structure and easy to operate, collects and analyzes pollen samples in an automatic and online mode, can reduce sample losses, reduces a large number of labor and time losses and can be used for routine atmosphere pollen monitoring.