Extracting the position of individual molecular probes with high precision is the basis and core of super-resolution microscopy. However, with the expectation of low-light conditions in life science research, the signal-to-noise ratio (SNR) decreases and signal extraction faces a great challenge. Here, based on temporally modulating the fluorescence emission at certain periodical patterns, we achieved super-resolution imaging with high sensitivity by largely suppressing the background noise. We propose simple bright-dim (BD) fluorescent modulation and delicate control by phase-modulated excitation. We demonstrate that the strategy can effectively enhance signal extraction in both sparsely and densely labeled biological samples, and thus improve the efficiency and precision of super-resolution imaging. This active modulation technique is generally applicable to various fluorescent labels, super-resolution techniques, and advanced algorithms, allowing a wide range of bioimaging applications.