Because of the influence of the curvature of cylindrical conformal array, the performance will be deteriorated and even become invalid when MUSIC algorithm is used to estimate signal's DOA. The problem that the steering vector and the noise subspace are not orthogonal is efficiently solved by reconstructing the steering vector with directional of array element in consideration of the carrier's block. By contrasting with sub-array divided technique, Monte Carlo simulation and verification are done, and the estimation performance of MUSIC algorithm is analyzed. Finally, by taking the multi-layer column for example, the DOA estimation for four sources from different orientations are simulated and verified. The simulation results show that the method has the advantages of high differentiation and precision, also demonstrate that the proposed scheme is efficient and of high estimation performance.