In order to reveal the secular deformation evolution and strain accumulation progress along subduction zone, we focus on high-precision Global Navigation Satellite System (GNSS) data processing, GNSS time series analysis and regional spatiotemporal filtering. The GNSS position time series is modeled as a combination of the long-term plate movements, short-term noise and the frequency-dependent variations and tectonic deformation information. Common Mode Errors (CME) is removed and the deformation signals is then extracted from the residual time series by Principal Component Analysis (PCA). Combing the filtered displacement array and the dynamic regional strain array derived from GNSS baseline, a spatiotemporal tectonic evolution map is exhibited obviously. We process the data recorded by GEONET over the 2003–2011 period in middle Japan island and reveal the dynamic evolution of crustal deformation along subduction zone. The results show that the regional reference frame transformation by constraining one site location and one stable GNSS baseline direction can further improve the Signal-to-Noise Ratio (SNR) of GNSS observations. A integrated analysis combining the baseline length with azimuth change can show the crustal motion feature more comprehensively. The observed behaviors agree well with the simulation experiment results of the rock rupture in the laboratory. We divide the pre-seismic deformation into four stages, the stable linear strain accumulation stage, the formation stage of the local locked area, local decoupling stage, and strain release stage. We also give an appropriate dynamical model for the interplate coupling to explain the observed deformation characteristics. Research result provides some of the observational new evidence for inter-seismic deformation anomaly detection and the medium- to longer-term seismic hazard assessments.