This paper analyzes and investigates the quality assessment of spoken English pronunciation using a cognitive heuristic computing approach and designs a corresponding spoken pronunciation quality assessment system for practical training. Using the general Goodness of Pronunciation assessment algorithm as a benchmark, the shortcomings of the traditional Goodness of Pronunciation method are explored through statistical experiments, and the validity of the overall posterior probability output from the speech model for pronunciation quality assessment is verified. For the analysis of rhythm, there is no common algorithm framework, but in this paper, the F0 similarity algorithm based on dynamic time regularization and the stop similarity algorithm based on forced alignment is proposed for the two main factors of rhythm, intonation, and pause, respectively. After framing, the Hamming window processing is used to make the signal smoother, reduce the side lobe size after fast Fourier transform processing, and solve the problem of spectrum leakage. Compared with the ordinary rectangular window function, the Hamming window can obtain a higher quality spectrum. And combined with CTC for speech recognition modeling, the recognition rates are comparable in the case of using BLSTM and bidirectional threshold cyclic unit BGRU as the hidden layer unit, respectively, and the training time is 23% less than BLSTM using BGRU; in addition, the BGRU-CTC model is improved by using a 2-BGRU-CTC model with 256 hidden layer nodes, so that the error rate of phoneme recognition is reduced to 33%. The effectiveness of the algorithm framework is also verified through experiments, which further proves the effectiveness of our proposed phoneme segment feature and rhyme similarity algorithm.