Preparation of defect‐free and optimized thin film nanocomposite (TFN) membranes is an effective way to enhance the process of organic solvent nanofiltration. However, it still remains a great challenge due to poor filler particle dispersibility in organic phase and compatible issue between fillers and polymers. Aiming at these difficulties, UiO‐66‐NH2 nanoparticles were surface modified with long alkyl chains and used in the preparation of TFN membranes. As a result, defect‐free TFN membranes with ultrathin MOF@polyamide layer were successfully prepared benefited from the improved particle dispersibility in n‐hexane. Significant enhancement was found in methanol permeance after nanoparticle incorporation, without comprising the tetracycline rejection evidently. Especially, the novel TFN membrane prepared with organic phase solution containing 0.15% (w/v) modified UiO‐66‐NH2 nanoparticles showed a superior methanol permeance of 20 L·m−2·h−1·bar−1 and a tetracycline rejection of about 99%, which is appealing to the application in pharmaceutical industry for example. © 2016 American Institute of Chemical Engineers AIChE J, 63: 1303–1312, 2017