In recent years, the response of fern gametophyte to enviroment has grabbed much attention in the academic community. However, studies on influence of plant invasion to fern gametophyte were scarce. It was increasingly recognized that allelopathy plays an important role in biological invasion. Hence, it is necessary to study the allelopathy of invasive plant to fern gametophyte and elucidate the mechanisms by which invasive plant causes phytotoxicity. As one of the main invasive plants in China, Bidens pilosa exhibited allelopathic effects on spermatophyte growth. Field investigation showed that many ferns were threatened by the invasion of B. pilosa. The distribution of Pteris multifida overlaps with that of B. pilosa in China. To examine the potential involvement of allelopathic mechanisms of root exudates in B. pilosa, changes in photosynthesis of P. multifida gametophyte were analyzed. We found that there were significant differences in photosynthesis between the control and B. pilosa exudates. Gametophyte of P. multifida exposed to B. pilosa had decreased quantum yield of photosystem II (Φ PSII ) electron transport. Meanwhile, lower quantum efficiency of open PSII reaction centers (Fv/Fm), photochemical fluorescence quenching (qP) and electron transport rate (ETR) were measured. The inhibitory effects increased with increasing exudate concentrations. At day 10, root exudates of B. pilosa exhibited the greatest inhibition. Non photochemical quenching (NPQ) was elevated in response to exudate treatments. Chl a, Chl b, carotenoid (Car) and the total chlorophyll decreased as exudate concentrations increased. These results suggest that the observed inhibitory or stimulatory effects on photosynthesis may have an adverse effect on P. multifida, and that allelopathic interference seems to participate in this process.