Waterlogging and shading result from continuous rain are the main meteorological disasters for wheat (Triticum aestivum L.) production. In order to evaluate the effects of waterlogging and shading on yield components of winter wheat (both independent and combined), pot experiments were conducted using two representative cultivars in local, Ningmai 13 and Yangmai 13. In total, 4 treatments, including CK (control), WA (waterlogging alone), SA (shading alone) and WS (both waterlogging and shading) were established with three duration (5, 10 and 15 d, respectively) at jointing and grain-filling stages. Results showed that, in the case of non-stressed environment, Yangmai 13 got a better production compared with Ningmai 13 (grain yield per plant was 14.25 g and 15.97 g for Ningmai 13 and Yangmai 13, respectively). However, compared with Yangmai 13, Ningmai 13 got a better yield under stresses at jointing stage, while a similar yield was observed when stresses are at grain-filling stage. By comparing wheat yield and its components, the negative effects of the stresses showed a tendency that WA > WS > SA at jointing stage, whereas WS > WA > SA at grain-filling stage. The result demonstrated that shading had a compensative effect on waterlogging at jointing stage while an addictive effect at grain-filling stage. Reduction of wheat production caused by continuous rain depended on the growth stages. Effect of growth stage on grain yield should be considered when waterlogging and shading packages of wheat growth model were established.