Supramolecular particle compositions based on medicinal natural products (MNPs), their synthetic analogs and derivatives, and methods to prepare and use them are provided. Five classes of MNPs and their derivatives including diterpene resin acid, phytosterol, lupane-type pentacyclic triterpene, oleanane-type pentacyclic tritepene, and lanostane-type triterpene form functional nano- or micro-structures that are stable to strong acidic environment and effectively penetrate the gastrointestinal tract. Therapeutic, prophylactic, or diagnostic agents that generally have poor intestinal permeability are converted to bioavailable forms when delivered with these supramolecular particles. Among many others, small compound chemotherapeutic agents and peptide therapeutics encapsulated therein have a much greater plasma concentration following oral administration, and effectively controls and treat symptoms associated with tumors or diabetes.