This paper proposes a novel method for simultaneous cell shape and motion analysis in rapid microchannel flows based on a multi-object feature extraction algorithm with a frame-straddling high-speed vision platform. This system can synchronize two camera inputs that share the same view with only a very small sub-microsecond time delay. Real-time video processing is performed using the hardware logic by extracting the moment features of multiple cells at 2000 fps or more, which are obtained from the two camera inputs, and their frame-straddling time can be adjusted from 0 to 0.5 ms in 9.9 ns steps. After setting the frame-straddling time within a certain range to avoid large image displacements between the two camera inputs, the frame-straddling high-speed vision platform can perform simultaneous shape and motion analysis of cells in fast microchannel flows of 1 m/s or greater. The results of real-time experiments conducted to analyze the deformabilities, velocities, and shapes of fast-flowing sea urchin egg cells in straight and L-type microchannels verified the efficacy of our vision-based cell analysis system.