H2O maser emission at 22 GHz in the circumstellar envelope is one of the good tracers of detailed physics and kinematics in the mass loss process of asymptotic giant branch stars. Long-term monitoring of an H2O maser spectrum with high time resolution enables us to clarify acceleration processes of the expanding shell in the stellar atmosphere. We monitored the H2O maser emission of the semi-regular variable R Crt with the Kagoshima 6-m telescope, and obtained a large data set of over 180 maser spectra over a period of 1.3 years with an observational span of a few days. Using an automatic peak detection method based on least-squares fitting, we exhaustively detected peaks as significant velocity components with the radial velocity on a 0.1 km s−1 scale. This analysis result shows that the radial velocity of redshifted and blue-shifted components exhibits a change between acceleration and deceleration on the time scale of a few hundred days. These velocity variations are likely to correlate with intensity variations, in particular during flaring state of H2O masers. It seems reasonable to consider that the velocity variation of the maser source is caused by shock propagation in the envelope due to stellar pulsation. However, it is difficult to explain the relationship between the velocity variation and the intensity variation only from shock propagation effects. We found that a time delay of the integrated maser intensity with respect to the optical light curve is about 150 days.