The Web-based Environment for Systems Engineering (wese) is a Web-based modeling and simulation environment in which the level of abstraction of a model can be configured statically (prior to simulation) or dynamically (during simulation) by substituting a module (set of components) with an equivalent component or vice versa through a process called dynamic component substitution (DCS). DCS can considerably improve the overall efficiency of simulations by enabling dynamic tradeoffs between several modeling and simulation related parameters. However, identifying ideal sequence of DCS is a complicated task. This paper proposes a novel methodology called DCS performance prediction methodology (DCSPPM) to identify ideal sequences of DCS. DCSPPM utilizes estimates of the changes induced by each atomic DCS along with model characteristics to predict the changes induced by a combination of substitutions. Our studies indicate that the proposed methodology provides good estimates (maximum error <8%) of the changes induced by DCS.