Peroxisome is a kind of organelle conserved in eukaryotes, which is involved in many biochemical metabolic processes, including β-oxidation of fatty acids, production and degradation of reactive oxygen species, etc. Peroxisome biogenesis has growth and division model and de novo biogenesis model, which involves the import of peroxisome matrix and membrane proteins. Under normal physiological conditions, the proliferation and degradation of peroxisomes are balanced. While the matrix protein and membrane proteins in the peroxisome are misfolded and excessively accumulated, or the peroxisome is under environmental stress, such as high reactive oxygen species (ROS) concentration was exhibited, the peroxisomes homeostasis will be unbalanced. In order to maintain homeostasis in the biogenesis process and environmental stress, the peroxisome through division and degradation for quality control. What’s more, peroxisome has evolved multiple degradation pathways, including pexophagy, the receptor accumulation and degradation in the absence of recycling (RADAR) depending on ubiquitin-proteasome system (UPS) and so on. These pathways of peroxisomal degradation are significant for maintaining the integrity of cell structure and function. As the metabolic hub of eukaryotic cells, peroxisomes exchange substances and transmits signals with other organelles through peroxisomal membrane contact sites (MCSs), such as mitochondria, endoplasmic reticulum, lysosome and so on. These peroxisomal MCSs play a vital role in metabolic functions and homeostasis regulation, including lipid metabolism, peroxisome division, autophagy and other biological processes. In recent years, the maintenance of peroxisome homeostasis and MCSs have become research hotspots at home and abroad. The quantity change and spatio-temporal distribution of peroxisome are regularly dynamic to maintain the organism’s normal life activities, while the homeostasis imbalance of peroxisome will result in serious physiological dysfunction of cells. In humans, more and more diseases have been confirmed to be related to the imbalance of peroxisome homeostasis or mutations of peroxisome membrane contact sites, including cancer, diabetes, Alzheimer’s disease and Parkinson’s disease. In plant pathogenic fungi, recent studies have proved that the key genes of peroxisome biogenesis play an important role in pathogenicity, such as of rice blast fungus. This paper reviews the recent advances in the mechanism of peroxisome homeostasis and MCSs.