Taking the flue-cured tobacco variety of "Longjiang 911" from Heilongjiang Province of Northeast China as test material, a pot experiment was conducted to study the effects of foliar spraying different concentration methyl jasmonate (MeJA) on the seedlings leaf chlorophyll content and chlorophyll fluorescence characteristics during the transplantation stage under drought and re-watering. Under drought condition, the leaf chlorophyll content, maximum fluorescence (F(m)), potential activities of PSII (F(v)/F(o)), maximum photochemical efficiency (F(v)/F(m)), actual photochemical efficiency (psi(PSII)), apparent electron transport rate (ETR), and photochemical quenching (q(P)) decreased, but the minimal fluorescence (F(o)) and non-photochemical quenching (q(N)) increased. Foliar spraying 0.2 and 0.5 mmol x L(-1) of MeJA had obvious positive effects in mitigating the decrease of F(v)/F(m), F(v)/F(o), phi(PSII), ETR, and q(P) and the increase of q(N) under drought stress, while spraying 1.0 mmol x L(-1) of MeJA had lesser effects. After re-watering, all the leaf chlorophyll fluorescence indices had obvious recovery, and spraying MeJA made the indices more close to the original levels before drought. It was suggested that foliar spraying MeJA could alleviate the degradation of chlorophyll and play definite role in protecting the PSII under drought stress, decrease the damage of drought stress on the seedlings, promote the rapid MeJA recovery of chlorophyll fluorescence parameters after re-watering, and thus, ensure the regrowth of flue-cured tobacco seedlings.