In recent years, the development and optimization of biodegradable coronary stents have become the research focus of many medical device manufacturers and scientific research institutions since they can be completely degraded and absorbed, and they restore vascular function. However, there is a lack of in situ quantification of these stents spatially in tissue in vivo. In this study, matrix-assisted laser desorption/ionization (MALDI) Fourier transform ion cyclotron resonance (FT ICR) and time-of-flight (TOF) mass spectrometric imaging (MSI) were used to analyze the time-dependent distributions of a biodegradable vascular scaffold, which consisted of copolymers of lactic acid and glycolic acid (PLGA) and its degradation products in cross-sections and longitudinal sections of blood vessels. The MALDI-MSI methods for analyzing the distribution of PLGA and its derivatives in vivo were established by optimizing the conditions of sample pretreatment and mass spectrometry (MS). In order to semi-quantify the contents of PLGA degradation products in blood vessels, self-made stainless-steel and indium tin oxide (ITO) target plates were developed to compare and establish the standard curves for semi-quantitative analysis. The target plate can be placed on the target carrier of MS simultaneously with the conductive slide, which can simultaneously carry out vapor deposition or spray on the substrate, to ensure the parallelism of the pretreatment experiments between the standards and the actual vascular samples. The proposed method provided a powerful tool for evaluating the distributions and degradation process of biological stent materials in the coronary artery, as well as provided technical support for the research and development of degradable biological stents and product optimization.