Using the Markov chain Monte Carlo (MCMC) method, we perform a global analysis constraining the dynamics of dark energy in light of the supernova (Riess "gold" samples), galaxy clustering (SDSS 3D power spectra and SDSS Lyman-α forest) and the latest three-year Wilkinson Microwave Anisotropy Probe (WMAP) observations. We have allowed the dark energy equation of state to get across -1 and pay particular attention to the effects when incorrectly neglecting dark energy perturbations. We find the parameter space of dynamical dark energy is now well-constrained with [Formula: see text]. Neglecting dark energy perturbations will make the parameter space of dark energy non-trivially smaller. The dynamical dark energy model where the equation of state crosses -1 is mildly favored and the standard ΛCDM model is still a good fit to the current data.