To estimate the Direction-of-Arrival (DOA) and Doppler frequency accurately and efficiently, a joint spectrum estimation method based on isolation niche technique and Shuffled Frog Leaping Algorithm (SFLA) was presented. Firstly, an extended observable matrix containing the information of DOAs and Doppler frequency was constructed by using state-space model. Then, the joint spectrum function was fitted using MUSIC algorithm and the extended observable matrix and the joint estimation were converted to multidimensional nonlinear function optimization. Finally, the isolation niche technique was applied to modification of the SFLA and the search of 2D MUSIC spectrum peak, so that to reduce the computation loads and obtain the estimated DOAs and Dopplers. Experimental results indicate that the Root Mean Square Errors(RMSEs) of DOAs and Dopplers estimated from the proposed method are 0.23°and 0.005 5 rad respectively when the signal source number is two and the SNR is 0 dB. The proposed method gets high resolution parameter estimation with less computation loads and control terms, and the parameters are paired automatically.