This study used Xinxin 2 (Juglans regia L. ‘Xinxin2’), a major cultivated walnut variety in Xinjiang, China, to clarify the response and adaptation mechanisms of the anatomical structures of walnut related to source–sink–flow under altered source–sink relationships. We anatomically observed the leaves, fruit stalks, and fruit of bearing branches by artificially adjusting the leaf-to-fruit ratio (LFR). The LFR substantially affected the leaf structure and thickness of the fruit-bearing branches obtained via girdled (p < 0.05). The results of the analysis of the leaf anatomy revealed that a low LFR impeded leaf growth and internal structural development while accelerating senescence, whereas a high LFR promoted leaf growth and delayed senescence. The same trend was observed for the phloem area (PA) of the fruit stalk with the increase in fruit load when the number of leaves on the fruit branch was the same. The maximum PA was reached when the number of fruits was high (except for 4L:3F). This indicates that the micro-anatomical structure of the fruit stalk is more developed under the treatment of a higher number of pinnate compound leaves and fruit level of LFRs. The cells of the 1L:3F and 2L:3F were considerably smaller in the green peel and kernel of the fruit on the branches obtained via girdled than those of 5L:1F plants (p < 0.05). No significant difference was found in the number of cells per unit area or the cross-sectional area of cells in the pericarp and kernel of the fruit under LFRs (p > 0.05); however, a large difference was noted in the microanatomical structure of the pericarp and kernel of fruit. Changes in the structural adaptation characteristics of walnut leaves (source), fruit stalk (flow), and fruit (sink) are related to source–sink regulation. A change in the LFR affects the carbohydrate synthesis in the leaves (source), transport in fruit stalks (flow), and the carbohydrate reception in fruits (sink).