The invention discloses natural compound modified asphalt and a preparation method thereof. The modified asphalt is prepared by utilizing the following materials according to the following weight parts: 30 parts to 95 parts of basic asphalt, 5 parts to 70 parts of Trinidad lake asphalt (TLA) and 1 part to 40 parts of rock asphalt. The method comprises the technical processes of: melting the basicasphalt at a temperature of 120 DEG C to 140 DEG C; melting the TLA at a temperature of 165 DEG C to 195 DEG C; and mixing the melted basic asphalt and the melted TLA and stirring the mixture of the basic asphalt and the Trinidad lake asphalt for 10 min to 50 min at ta temperature of 165 DEG C to 195 DEG C, and adding rock asphalt powder in the stirring process so as to obtain the finished product. The modified asphalt can improve temperature sensibility, increase the stability, deformation resistance, toughness, cracking resistance performance, anti-fatigue and cracking-resistant strength and durability, prolong the service life of the road and reduce the time for maintenance and overhaul and the maintenance cost; simultaneously the modified asphalt has excellent environment-friendly performance and can reduce pollution generated in the production process of a polymer modifier.