X-ray luminescence computed tomography (XLCT) is a new hybrid imaging modality, which has the capability to improve optical spatial resolution to hundreds of micrometers for deep targets. In this paper, we report a multiple pinhole collimator based microscopic X-ray luminescence computed tomography (microXLCT) system for small animal imaging. Superfine collimated X-ray pencil beams are used to excite deeply embedded phosphor particles, allowing us to obtain sub-millimeter optical spatial resolution in deep tissues. Multiple collimated X-ray beams are generated by mounting an array of pinholes in the front of a powerful X-ray tube. With multiple X-ray beams scanning, the phosphor particles in the region of the multiple beams are excited simultaneously, which requires less scanning time compared with a single beam scanning. The emitted optical photons on the top surface of the phantom are measured with an electron multiplying charge-coupled device (EMCCD) camera. Meanwhile, an X-ray detector is used to determine the X-ray beam size and position, which are used as structural guidance in the microXLCT image reconstruction. To validate the performance of our proposed multiple pinhole based microXLCT imaging system, we have performed numerical simulations and a phantom experiment. In the numerical simulations, we simulated a cylindrical phantom with two and six embedded targets, respectively. In the simulations, we used four parallel X-ray beams with the beam diameter of 0.1 mm and the beam interval of 3.2 mm. We can reconstruct deeply embedded multiple targets with a target diameter of 0.2 mm using measurements in six projections, which indicated that four parallel X-ray beam scan could reduce scanning time without comprising the reconstructed image quality. In the phantom experiment, we generated two parallel X-ray beams with the beam diameter of 0.5 mm and the beam interval of 4.2 mm. We scanned a phantom of one target with the two parallel X-ray beams. The target was reconstructed successfully, which indicated that multiple collimated X-ray beam scan approach is feasible in small animal imaging.