The invention relates to a small-sized intersecting structure relative position accurate measurement method. The method comprises the steps of manufacturing a measurement clamp of high coaxiality, the measurement clamp having an outer circumferential diameter matching the inner diameter of an intersecting element; enabling the measurement clamp to extend along the axial direction of the intersecting element into a fixing position of the intersecting element; using an optical projection measurement instrument for measuring the center of the intersected element and determining the center position of a part to be measured; meanwhile, measuring data of points of a contour in the portion that the measurement clamp extends into the intersected element; and analyzing the measured data, determining the center of the clamp by using a coordinate of a portion of the clamp into the intersected element, equivalently determining the center of the clamp as the axis of the intersecting element, thus measuring the position accuracy between the two elements of an intersecting structure indirectly, and determining whether the direction and position between the two elements of the intersecting structure conform to designing requirements. The method of the invention can achieve accurate and convenient measurement and analysis of the relative position of the elements of the intersecting structure, and improves the accuracy, effectiveness and consistency.