To investigate diverse information associated with the same sample, it's crucial to develop a multi-block data analysis. This study utilized quality parameters (L*, a*, b*, hardness, weight loss, vitamin C, titratable acid and soluble solid content), visible near-infrared (Vis-NIR) spectra and proton nuclear magnetic resonance (1H NMR) fingerprints to characterize the quality of Eureka lemons at different storage periods. Common Dimension (ComDim) multi-block analysis was carried out to explore the relationships between these multiple data blocks and assess the contribution of each block. Specifically, the ComDim method calculated the significance, scores, and loadings for each dimension to reveal the synergistic effects among multiple data blocks. Meanwhile, a data-fusion based principal component analysis was performed but was not as efficient as ComDim in exploiting multiple data blocks. The ComDim results indicated that Eureka lemons stored for less than 120 days were linked to firmness, the spectral region of 479–772 nm, and 1H NMR signals (sucrose, fucose, fructose, and α-glucose). Lemons stored for over 150 days correlated with L*, a*, b* values, weight loss, nutritional parameters, the spectral regions of 400–479 nm and 772–1000 nm, and 1H NMR signals (ethanol). This work demonstrates that ComDim furnishes a new approach to comprehensively evaluate the quality of Eureka lemons across storage periods. It also provides guiding significance for transportation, refrigeration and preservation of fruits or other agricultural products.