Many Evolutionary Algorithm (EA) based methods have been proposed to solve protein structure prediction (PSP) problem in HP-lattice model. One of common difficulties of those methods is the existence of invalid individuals produced by geometrical constraints in the conformation of protein (i.e. self-avoidance in the chain). A backtracking method is often used to repair the invalid individuals of genetic search in those methods. However, there is a disadvantage in basic backtracking method, the repairing computational cost is very heavy for long sequence instances. This paper proposes an improved backtracking-based repairing method for long sequence protein folding. A detection procedure is added in backtracking method to avoid entering invalid closed areas when selecting directions for the residues. Experimental results show that the proposed method can significantly reduce the number of backtracking searching operations and the computational cost for the long protein sequences.