In order to screen cocoa breeding materials with excellent fruit traits, pulp and cocoa bean quality, 17 indicators including fruit quality, fruit shell quality, fruit length, fruit width, fresh quality of seeds, pulp content, soluble sugar, total acid, pH, sugar-acid ratio, pulp sensory evaluation (aroma, sour-sweet taste, acceptance), cocoa butter, theobromine, caffeine, and polyphenols were measured for 11 cocoa germplasm. Principal component analysis and cluster analysis were used to comprehensively evaluate the 17 indicators of different cocoa germplasm fruits. The results indicated that the coefficients of variation (CV) for the 17 indicators ranged from 4.16% to 52.91%, with an average of 16.73%. Notably, caffeine exhibited the highest CV among all indicators. The CVs for pulp content, total acid, sugar-acid ratio, and caffeine were all above 20%, suggesting significant variations in fruit traits and quality among the 11 cocoa germplasms. This rich genetic diversity indicates a vast potential for the selection and improvement of cocoa cultivars with desirable characteristics. In the sensory evaluation of cocoa pulp, variety Xiangke 16 scored the highest, followed by TAS420 and TAS1413. Furthermore, the acceptability among testers was primarily influenced by the balance of sweetness and sourness in the pulp. Correlation analysis revealed that there were mainly positive correlations between fruit traits and pulp quality, while there were primarily negative correlations between cocoa bean quality traits and both fruit traits and pulp quality. In the principal component analysis, a total of five principal components with eigenvalues greater than 1 were extracted, accounting for a cumulative contribution rate of 89.521%. Based on the principal component scores of each indicator, a comprehensive ranking was conducted, with TAS420, Xiangke 16, and TAS414 scoring the highest. The three cocoa germplasm exhibited superior performance in fruit traits, pulp quality, and cocoa bean quality. Principal components 1 and 2 played crucial roles in the comprehensive evaluation. Among them, indicators such as pH, sugar-acid ratio, sensory evaluation, fruit quality, fruit shell quality, and fruit width contributed significantly to the evaluation of cocoa fruits. Based on the cluster analysis, the 11 cocoa germplasms were subdivided into four groups. Group I consisted of TAS1413, which exhibited superior fruit traits and pulp quality but had the poorest cocoa bean quality. Groups II and III comprised the top four germplasm in the comprehensive ranking, demonstrating excellent overall indicators and serving as important materials for breeding superior varieties. The remaining six germplasm belonged to Group IV, which had relatively average fruit traits and quality. This study would provide a foundation for the breeding of superior cocoa varieties, contributing to the diversification and development of the cocoa industry.