Abstract: Waterlogging is one of the most common factors limiting crop production of wheat-rice system in southern China. Wheat varieties 'Chuanmai104' and 'Neimai836' were used in 2011 2013 growing season to study chlorophyll fluorescence parameters of flag leaf and grain-filling properties of wheat under waterlogging at different growth stages (tillering, jointing, booting and grain-filling stages, with waterlogging duration of 35 days). The study explored the photosynthetic capacity and grain-filling traits under waterlogging in the region. Relative chlorophyll content (SPAD reading) and chlorophyll fluorescence parameters were measured using SPAD-502 and photon systems instruments, grain-filling process under waterlogging at different growth stages were fitted with Richard's equation. The results showed little change over time in SPAD value and chlorophyll fluorescence parameters (F_v/F_m, F_v/F₀, ΦPSⅡ, qP and NPQ) at 15 and 25 days after anthesis. However, sharp decreases in F_v/F_m, F_v/F₀ and ΦPSⅡ and obvious increase in NPQ were noted at 35 days after anthesis. There was no significant difference between waterlogging treatments and CK in terms of SPAD reading and chlorophyll fluorescence parameters (F_v/F_m, F_v/F₀, ΦPSⅡ and qP) 15 and 25 days after anthesis. Also 35 days after anthesis, waterlogging at tillering stage and grain-filling stage increased SPAD, F_v/F_m, F_v/F₀, ΦPSⅡ and qP, and decreased NPQ, compared with CK. Waterlogging at tillering and grain-filling stages had less effect on grain-filling, while waterlogging at jointing and booting stages improved grain-filling rate while shorten grain-filling duration resulting in lower grain weight. Grain weight had significant positive correlation with SPAD, but not significantly correlated with grain-filling rate. Grain weight was also significantly correlated with effective grain-filling duration and active grain-filling duration. This was especially obvious for fast-increasing and slowly-increasing grain-filling periods. 'Chuanmai104' had higher SPAD and F_v/F_m, F_v/F₀, ΦPSⅡ and qP. In the study area, it was necessary to pay more attention to waterlog draining at jointing and booting stages to ensure higher photosynthetic capacity, longer grain-filling duration and higher grain weight.