Aims. We aim for a better understanding of gas properties in the circum-nuclear disk (CND) region of the nearby gas-rich Seyfert 2 galaxy NGC 1068. We focus on line identification and the basic physical parameters estimation of molecular gas in the CND region. Methods. We used the IRAM 30 m telescope to conduct deep millimeter spectroscopy observations toward the center of NGC 1068. Results. Thirty-two lines were detected in this galaxy, 15 lines of wich were detected for the first time. With a sensitivity better by about a factor of 4 than observations in the literature for this source at 3 mm band, we detected several weak lines for the first time in this source, such as lines from CH₃CCH, CH₃OCH₃, and HC¹⁸O⁺. Column densities of these molecules were estimated based on line emissions. Some marginal detections in the literature, such as HN¹³C (1–0), were confirmed. CH₃OCH₃ was detected for the first time in external galaxies. Lines from several carbon chain molecules and shock-related molecules were also detected in this source.