A new method to refine crystal structural parameters using convergent-beam electron diffraction (CBED), which is applicable to nanometre-size crystal structure analysis, is proposed. This method is based on the fitting between theoretical calculations and experimental intensities of energy-filtered two-dimensional CBED patterns containing higher-order Laue-zone (HOLZ) reflections. The use of HOLZ reflections is essential for the method because small displacements of atoms can be sensitively detected using HOLZ reflections with large reciprocal vectors. For this purpose, a new Omega-filter transmission microscope (JEM-2010FEF), which can take energy-filtered CBED patterns up to a high angle with a small distortion, and a new analysis program to refine structural parameters, which is based on many-beam Bloch-wave calculations and nonlinear least-squares fitting, have been developed. As a test example, a positional parameter and isotropic and anisotropic Debye-Waller factors of CdS have been refined. Two-dimensional CBED patterns calculated with the refined parameters show very good agreement with the experimental ones, and the refined values of the parameters also agree well with the result of a single-crystal X-ray diffraction experiment. Important problems of the analysis procedure are discussed item by item.