•Eight 3-D structures (3DS) are designed and circulating pebble flows are studied.•Constructing two new indices to analyze the mixing of the upper and lower pebbles.•3DS impedes near wall pebble flow, increases cycling speed and mixing at the core.•Triangular/helicoidal 3DS are better in speeding up and enhancing mixing.•Saturation phenomenon for the number of structural grooves in 3DS is found. The pebbles’ movement in the pebble beds of 10 MW high-temperature gas-cooled test reactor (HTR-10) presents as a kind of circulating quasi-static dense pebble flow. The mixing of the upper and the lower fuel pebbles is important because the fast and good mixing is beneficial to flattening the power distribution and lowering the maximum temperature in the lower part of the pebble bed, where the temperature is higher than other region because of the higher burn-up of fuel pebbles. To figure out the effect of different three-dimensional (3-D) wall structures on the flow and mixing of pebbles, eight 3-D wall structures are designed and mono sized pebbles with same density are adopted to simulate by discrete element method (DEM). With phenomenological methods and different mixing indices, qualitative and quantitative analysis are performed and presented hereinafter. All selected wall structures have different degrees of effect on impeding the pebble flow near the wall, accelerating the cycling speed of pebbles at the core region and strengthening the mixing of the upper and lower pebbles in the pebble bed. Compared with the designed trapezoidal and plane structures, triangular and helicoidal structures perform better in accelerating the cycling speed for pebbles at the core region and strengthening the mixing of pebbles by analyzing cycle index (CI), coordination-Lacey’s rule mixing index (CLMI) and coordination-concentration based mixing index (CCMI). In addition, a phenomenon of saturation for the number of structural grooves is reported in this literature. That is, the effect of accelerating the cycling speed of pebbles at core zones and strengthening the mixing gets closer to a certain degree if we make the different grooves denser. The optimal structure to accelerating cycling speed for pebbles in core zones and improving mixing is triangular structure among the four kinds of structures, while the optimum solution for the number of grooves requires deeper investigation.