Understanding the correlations between magnetic skyrmions and the microstructural characteristics of the crystals that host skyrmions is a key issue for fundamental research and practical applications of novel type of magnetic materials. Magnetic skyrmion has received great attention due to its non-trivial topological properties and stability. Here we focus on two important points:1) dimensional confinement effects on magnetic skyrmions in magnetic nanostructures, specifically, the magnetic evolution, its related topological properties and energetic stability in confined nanostructured geometries; 2) effects of crystallographic defects on magnetic skyrmions, such as the pinning effect of magnetic skyrmion by crystal defects, and the effect of crystallographic-magnetic chirality reversal at crystal grain boundaries. For the study of dimensional effects on skyrmions in confined nanoscale geometries, we use state-of-the-art electron holography to directly image the morphology and nucleation of magnetic skyrmions in a wedge-shaped FeGe nanostripe that has a width in a range of 45-150 nm. Our experimental results reveal that geometrically-confined skyrmions are able to adopt a wide range of sizes and ellipticity in a nanostripe, which are not existent in thin films nor bulk materials and can be created from a helical magnetic state with a distorted edge twist in a simple and efficient manner. We further perform micromagnetic simulations to confirm our experimental results. The flexibility and ease of formation of geometrically confined magnetic skyrmions may help to optimize the design of skyrmion-based memory devices. For studying the effects of crystallographic defects on magnetic skyrmions, we use in situ Lorentz microscopy and off-axis electron holography to investigate the formation and characteristics of skyrmion lattice defects and their relationship to the underlying crystallographic structure of a B20 FeGe thin film. The measurements of spin configurations at grain boundaries reveal the crystallographic and magnetic chirality across adjacent grains, resulting in the formation of interface spin stripes at the grain boundaries. In the absence of material defects, our results show that skyrmion lattices possess dislocations and domain boundaries, in analogy to atomic crystals. Moreover, the distorted skyrmions can flexibly change their size and shape to accommodate local geometry, especially at sites of dislocations in the skyrmion lattice. These findings offer an insight into the elasticity of topologically protected skyrmions and their correlation with underlying material defects. Our electron holography results provide a quantitative determination of the fine skyrmionic spin textures in magnetic nanostructures. The resolved spin textures will be correlated with the material microstructures to provide important information about the relationship between the magnetic functions and the material microstructures. Our experiments also highlight the applicability of state-of-the-art electron holography for the study of complex spin textures in nanostructures.