We review the advancement of nonstationary time series analysis from the perspective of Cowles Commission structural equation approach. We argue that despite the rich repertoire nonstationary time series analysis provides to analyze how do variables respond dynamically to shocks through the decomposition of a dynamic system into long-run and short-run relations, nonstationarity does not invalid the classical concerns of structural equation modeling — identification and simultaneity bias. The same rank condition for identification holds for stationary and nonstationary data and some sort of instrumental variable estimators will have to be employed to yield consistency. However, nonstationarity does raise issues of inference if the rank of cointegration or direction of nonstationarity is not known a priori. The usual test statistics may not be chi-square distributed because of the presence of unit roots distributions. Classical instrumental variable estimators have to be modified to ensure valid inference.