The charge transfer inefficiency (CTI) of the X-ray CCDs on board the Suzaku satellite (X-ray Imaging Spectrometers; XIS) has increased since the launch due to radiation damage, and the energy resolution has been degraded. To improve the CTI, we have applied a spaced-row charge injection (SCI) technique to the XIS in orbit; by injecting charges into CCD rows periodically, the CTI is actively decreased. The CTI in the SCI mode depends on the distance between a signal charge and a preceding injected row, and the pulse height shows periodic positional variations. Using in-flight data of onboard calibration sources and of the strong iron line from the Perseus cluster of galaxies, we studied the variation in detail. We developed a new method to correct the variation. By applying the new method, the energy resolution (FWHM) at 5.9 keV at March 2008 is ~155 eV for the front-illuminated CCDs and ~175 eV for the back-illuminated CCD.