To predict the degradation of engine maneuvering characteristics, transient process based gas path analyses were conducted. Sequential Operating Points Analysis (SOPA), which extracts more information from a limited number of gas path sensors as well as eliminate the systematic error introduced by the averaging effect of multiple operating points approach, was applied to the estimation of a large number of health parameters. To solve the convergence problem of health parameter estimating calculation with considerable deviations, indirectly recursive Newton-Raphson method enhanced non-dominated sorting differential evolution algorithm was introduced. Applications to a dual-spool separated flow turbofan engine indicated that the proposed approach was able to predict a large number of health parameters with considerable deviations, using transient measurements provided by a very limited number of gas path sensors, efficiently and accurately.