The design of the three-dimensional (3D) porous structures and surface morphological/topographies of implants is considered as a novel approach to enhance the bioactivity and osteoinductive ability in the field of bone regeneration. In the present study, highly interconnective macroporous hydroxyapatite (HAp) bioceramic scaffolds with nanosheet, nanorod and micro-nano-hybrid (the hybrid of nanorod and microrod) surface topographies were fabricated using α-tricalcium phosphate (α-TCP) ceramic scaffolds as precursors, through regulation of the hydrothermal reaction conditions. Moreover, the effects of these three surface topographies on attachment, proliferation and osteogenic differentiation of rat bone marrow stromal cells (bMSCs) as well as the related mechanisms were systematically investigated. The results showed that the HAp bioceramics with these micro-/nano-topography surfaces significantly enhanced cell attachment, cell viability, alkaline phosphatase (ALP) activity, and mRNA expression levels of osteoblast-related genes of bMSCs. In particular, the biomimetic feature of the micro-nano-hybrid topography surface possessed the highest stimulatory effect. The activation in extracellular signal-related kinases (ERK), and p38 mitogen-activated protein kinase (MAPK) signaling pathways was observed in bMSCs cultured on HAp bioceramics with micro-/nano-topography surfaces especially for the micro-nano-hybrid topography surface, and these enhancement effects could be blocked by ERK inhibitor PD98059, and P38 inhibitor SB203580, respectively. Moreover, the in vivo bone regeneration results of rat critical-sized calvarial defect models confirmed that macroporous HAp bioceramics with these micro-/nano-topography surfaces could promote new bone formation and mineralization as compared with the control HAp bioceramic with traditional smooth surfaces, while the scaffold with a micro-nano-hybrid surface could achieve a better effect. The study suggests that the hierarchical micro-nano-hybrid topography shows immense potential in improving the clinical performance of macroporous HAp bioceramics.