Ordinary differential equations (ODEs) are widely used to model the dynamic behavior of a complex system. Parameter estimation and variable selection for a "Big System" with linear ODEs are very challenging due to the need of nonlinear optimization in an ultra-high dimensional parameter space. In this article, we develop a parameter estimation and variable selection method based on the ideas of similarity transformation and separable least squares (SLS). Simulation studies demonstrate that the proposed matrix-based SLS method could be used to estimate the coefficient matrix more accurately and perform variable selection for a linear ODE system with thousands of dimensions and millions of parameters much better than the direct least squares (LS) method and the vector-based two-stage method that are currently available. We applied this new method to two real data sets: a yeast cell cycle gene expression data set with 30 dimensions and 930 unknown parameters and the Standard & Poor 1500 index stock price data with 1250 dimensions and 1,563,750 unknown parameters, to illustrate the utility and numerical performance of the proposed parameter estimation and variable selection method for big systems in practice.