To develop an efficient, sustainable, and eco-friendly biobased flame-retardant microcapsule suitable for the working environments of tunnel asphalt pavement and reveal its flame-retarding mechanism on asphalt combustion, microencapsulated amylopectin (MAMP) was first prepared using an in situ polymerization method. Changes in the basic properties of amylopectin (AMP) and its compatibility with asphalt after microencapsulation were studied. Then, the flame retarding efficiency and improvement effects of MAMP on the flame retardancy of asphalt were investigated. Results show that melamine formaldehyde (MF) resin is evenly coated on the AMP surface without changing the chemical composition of AMP, increasing the thermal stability of AMP and the compatibility between AMP and asphalt. MAMP reacts with ammonium polyphosphate (APP) to release a number of incombustible gases to delay asphalt combustion at early stages and subsequently dehydrates to form a stable starch-based charring layer to suppress heat and mass transfer during asphalt combustion, improving the fire safety of asphalt materials. The added 3% MAMP can reduce the total enthalpy value of all exothermic peaks of the 10% APP-modified asphalt by 43.6%. As a carbonization agent, MAMP produces a charring layer with higher heat capacity during asphalt combustion, exerting an excellent inhibition effect on heat release. This study provides a reference for the application of biobased materials in flame-retarded asphalt pavements.