Single photons are the best carriers of quantum information for long-distance transmission. Nevertheless, maximal achievable distance is limited by the exponential decay of photons as a function of link length. The protocol of quantum repeater provides a promising solution by replacing direction transmission with segmented entanglement distribution and entanglement connection via swapping. The quantum repeater necessitates a key element of quantum memory for making efficient interconnections. An atomic ensemble is very suitable for this purpose due to the collective enhanced interaction. Single photons are stored as collective excitations in an atomic ensemble. Thus a comprehensive study of the physics relating to collective excitations is crucially important for improving the quantum memory performance and its reachable applications in quantum repeater and quantum network. In this article, we review our experimental work on cold atomic ensembles in recent years, focusing on the coherent manipulation of collective excitations. We first briefly introduce the general concept of collective excitations and the preparation process through spontaneous Raman scattering, and we review our experimental work on extending the coherence time, such as suppressing motional dephasing by increasing the spin-wave wavelength, by confining atoms with a three-dimensional optical lattice. Afterwards, we discuss about the retrieval process of collective excitations and review our experiments on using a ring-cavity enhanced setup to improve the retrieval efficiency. The coherent qubit operation in a quantum memory is very useful for enabling new functionalities for a quantum network, in a subsequent section, we thus review our work on developing Raman-based coherent operations for single excitations. Afterwards, we mention our experiments on creating a pair of atom-photon entanglement by interfering two modes of a collective excitation. Improving the entanglement preparation efficiency is crucially important, and Rydberg-based interaction provides a promising solution. Our experimental work in this direction is also reviewed. Additionally, as an application in coherent manipulation with collective excitations, we show several experiments on using excitations in remote atomic memories and demonstrating basic functionality of quantum repeater and quantum network. In short, significant progress has been made in the coherent manipulation of single collective excitations in cold atomic ensembles, and further improvement will be accelerated by the Rydberg-enabled interactions; practical applications in quantum repeater and quantum network is foreseeable in the near future.