Constipation and hemorrhoids often co-occur and are causally related. Natural products exhibit unique advantages in the prevention and treatment of both diseases due to their multi-target and multi-pathway characteristics. This review systematically summarizes the mechanisms, formulation innovations, and clinical applications of natural products for constipation and hemorrhoids. For constipation, the mechanisms include: physical expansion and hydration to increase fecal bulk and soften stool; regulation of intestinal fluid metabolism, neurotransmitter release, and interstitial cells of Cajal (ICC) function to promote peristalsis; and modulation of gut microbiota. For hemorrhoids, the mechanisms include: enhancing venous tone, improving microcirculation, inhibiting the NF-κB/NLRP3 inflammatory pathway, and promoting tissue repair. Psyllium, quercetin, curcumin, and others exhibit dual benefits. Novel formulations such as microemulsion gels, nanogels, and effervescent suppositories have improved bioavailability. Combination therapies with physical modalities or chemical drugs have shown evidence-based benefits. However, challenges remain, including complex composition, extraction difficulties, unclear mechanisms, and a lack of high-quality clinical studies. Future efforts should focus on improving extraction processes and quality control, employing network pharmacology and multi-omics to elucidate mechanisms, conducting rigorous clinical trials, and promoting the translational application of natural products.