Percutaneous coronary intervention with stenting is the most widely adopted surgical technique for the treatment of coronary disease. However, in-stent restenosis (ISR) continues to cause serious concern. Improving the functionality of endothelial cells (ECs) is of importance for dealing with ISR. However, limited successes in in vivo studies imply that the underlying mechanism relating to the process of intervention with a material has not been well understood to date. Another determining factor that has long been underestimated in the design of stents is immune response dominated by macrophages (MΦs). In the present study, TiO2 nanotube arrays (TNAs) with different diameters were fabricated by anodization. The diameter could be precisely adjusted from 15 nm (Nano-15) to 120 nm (Nano-120). The effect of distinct nanodimensions on the behavior of ECs/MΦs and their crosstalk was investigated. The results indicated that Nano-15 not only promoted the initial vitality of ECs and function-related gene expression but also enhanced the activation and spread of MΦs. In addition, Nano-15 downregulated the gene expression of inflammatory cytokines and pro-inflammatory M1 markers, while upregulating the gene expression of pro-healing M2 markers, autophagy markers, and growth factors of MΦs. A further investigation conducted using a specialized specimen-conditioned medium (SCM) from MΦs/ECs disclosed that the SCM derived from Nano-15 was able to manipulate a favorable microenvironment to facilitate MΦ-EC crosstalk via downregulation of inflammation-related gene expression and upregulation of function-related gene expression in ECs. Moreover, we further investigated the hemocompatibility of specimens in an ex vivo animal model. The results indicated that both pure Ti and Nano-15 possess satisfactory hemocompatibility, as manifested by the few thrombi that formed around the specimens. Additionally, in comparison with Nano-120, Nano-15 can significantly alleviate platelet activation and manipulate a loose structure of fibrin fibers in a dynamic situation. This study suggests that the application of Nano-15 as a surface coating for coronary stents may be a promising strategy for preventing ISR.