The invention discloses a flame-resistant modified nylon 56 polymer and a preparation method thereof. The method comprises the following steps that 1, bio-based pentane diamine reacts with adipic acid in water under protection of nitrogen to obtain a nylon 56 saline solution, wherein bio-based pentane diamine is obtained by removing two carboxyl-terminated groups from lysine or lysinate under the action of lysine decarboxylase; 2, the nylon 56 saline solution, a molecular weight regulator and a flame retardant are added into a reaction vessel, pressure maintaining is conducted at the temperature of 210 DEG C to 240 DEG C under the pressure of 1.7 MPa to 1.85 MPa, the pressure in the reaction vessel is released, the temperature is increased to 265 DEG C to 275 DEG C, vacuumizing and stirring are conducted, and then the flame-resistant modified nylon 56 polymer is obtained. Compared with products such as common nylon 66 and nylon 6, the flame-resistant modified bio-based nylon 56 prepared through the method has the greatest advantages of achieving the flame retarding and melting drop resisting characteristics and being suitable for being used at high-temperature, high-humidity and high-voltage places, safe and environmentally friendly; in addition, due to the fact that the physical property is not obviously reduced in the modification process, so that subsequent further modifying, processing and manufacturing are conveniently conducted.