Materials with defined porous structures have drawn considerate attention for decades. Most of these materials display similar porous structure within the entity. Sometimes materials with different surface and internal structures would be appreciated. In the present study, a microporous silica material with surface macroporous arrays was prepared by a sol-gel technique combined with a template method. The sol was prepared via hydrolysis of tetraethoxylsilane by hydrochloric acid. To this sol, monodispersed, hydrophobic polystyrene spheres were added. By ultrasonication, the spheres floated and assembled to regular arrays on the aqueous sol surface. At low temperature, the sol was gradually gelated, which froze the spheres in-situ. By washing with toluene, the polystyrene spheres were dissolved, leaving aligned arrays on the surface of the gel. The macropores can be easily controlled by selecting particles with suitable sizes. The material would find application in catalysis, sensor and adsorption.