Focal stack (FS) is an effective technique for fast 3D imaging in high-resolution scanning transmission X-ray microscopy. Its crucial issue is to assign each object within the sample to the correct position along the optical axis according to a proper focus measure. There is probably information loss with previous algorithms for FS reconstruction because the old algorithms can only detect one focused object along each optical-axial pixel line (OAPL). In this study, we present an improved FS algorithm, which utilizes an elaborately calculated threshold for normalized local variances to extract multiple focused objects in each OAPL. Simulation and experimental results show its feasibility and high efficiency for 3D imaging of high contrast, sparse samples. It is expected that our advanced approach has potential applications in 3D X-ray microscopy for more complex samples.