Biocompatible porous scaffolds with tunable microstructures and drug delivery ability have aroused increasing attention in the application of the biomedical fields, especially in tissue engineering. In this study, we have facilely fabricated the poly(L-lactic acid)-modified halloysite nanotubes (m-HNTs)/poly(E-caprolactone) (PCL) porous scaffolds by direct solvent evaporation of m-HNTs stabilized water in oil Pickering emulsion templates, which contain PCL in the oil phase. The obtained scaffolds have possessed the porous microstructures, which can be easily tailored by varying the preparation conditions of emulsion templates including m-HNTs concentrations and the volume ratios of water to oil. Furthermore, the antibacterial drug enrofloxacin (ENR) has been loaded into the scaffolds, and the in vitro release studies show the potential of m-HNTs/PCL porous scaffolds as drug carriers. And the antimicrobial test results have proved that the ENR-loaded porous scaffolds exhibit obvious and long-term antibacterial activity against Escherichia coli. In addition, mouse bone mesenchymal stem cells (mBMSCs) are cultured on the m-HNTs/PCL porous scaffolds, and the results of cell counting kit-8 assay and confocal laser scanning microscope observation show that the m-HNTs/PCL porous scaffolds are cytocompatible, because mBMSCs can attach, develop and proliferate well on the porous scaffolds. All the results indicate that the m-HNTs/PCL porous scaffolds hold great potential applications in tissue engineering as scaffolds and/or drug carriers.