Although there are many studies on code optimization of the joint source-channel coding (JSCC) system based on double protograph low-density parity-check codes with the joint belief propagation (JBP) algorithm, but it is still unknown whether the source code and channel code (as a code pair) can perform well when the joint shuffled scheduling decoding (JSSD) algorithm is adopted. In this letter, two decoding threshold analysis algorithms, including joint shuffled protograph extrinsic information transfer (PEXIT) and source shuffled PEXIT algorithm, are proposed to calculate joint/source decoding thresholds for this system with the JSSD algorithm. With the proposed algorithms, it is found that the optimized code pairs for this system with the JBP algorithm may not perform well with the JSSD algorithm, implying that code pair with the JSSD algorithm needs to be redesigned. Then, a two-stage optimized framework is proposed to design the code pair for this system with the JSSD algorithm. Simulations and decoding threshold analysis both show that the proposed code pair for this system with the JSSD algorithm can obtain lower error floor and better waterfall performance than the existing code pairs.