This paper proposed a novel spatial frequency analysis method for the investigation of potassium dihydrogen phosphate (KDP) crystal surface based on an improved bidimensional empirical mode decomposition (BEMD) method. Aiming to eliminate end effects of the BEMD method and improve the intrinsic mode functions (IMFs) for the efficient identification of texture features, a denoising process was embedded in the sifting iteration of BEMD method. With removing redundant information in decomposed sub-components of KDP crystal surface, middle spatial frequencies of the cutting and feeding processes were identified. Comparative study with the power spectral density method, two-dimensional wavelet transform (2D-WT), as well as the traditional BEMD method, demonstrated that the method developed in this paper can efficiently extract texture features and reveal gradient development of KDP crystal surface. Furthermore, the proposed method was a self-adaptive data driven technique without prior knowledge, which overcame shortcomings of the 2D-WT model such as the parameters selection. Additionally, the proposed method was a promising tool for the application of online monitoring and optimal control of precision machining process.