Thanks vincent Ogloblinsky for the help, we will be able to achieve this by using the --extTheme option and have to specify our custom theme as well and for the --theme we have to specify the custom flag name that we provided earlier.

Example:-

compodoc -p .\tsconfig.doc.json -y compodoc_theme/  -s --hideGenerator --disableSourceCode --disableDomTree --disableTemplateTab --disableStyleTab --disablePrivate --theme compodoc_lightmode

Here compodoc_theme my directory which contain my custom there. What happened internally is that compodoc will copy the styles inside the specified directory into the documentation/styles and from there using the --theme it will override the default dark theme.

Example for a sample custom theme file:

  body {
    background: #fafafa;
    color: #212121;
}

code {
    color: #e09393;
}

a,
.menu ul.list li a.active {
    color: #7fc9ff;
}

.menu {
    background: #fafafa;
    border-right: 1px solid #444;
}

.menu ul.list li a {
    color: #212121;
}

.menu ul.list li.divider {
    background: #444;
}

.xs-menu ul.list li:nth-child(2) {
    margin: 0;
    background: none;
}

.menu ul.list li:nth-child(2) {
    margin: 0;
    background: none;
}

#book-search-input {
    background: #fafafa;
    border-top: 1px solid #444;
    border-bottom: 1px solid #444;
    color: #212121;
}

.table-bordered {
    border: 1px solid #444;
}

.table-bordered > tbody > tr > td,
.table-bordered > tbody > tr > th,
.table-bordered > tfoot > tr > td,
.table-bordered > tfoot > tr > th,
.table-bordered > thead > tr > td,
.table-bordered > thead > tr > th {
    border: 1px solid #444;
}

.coverage a,
.coverage-count {
    color: #212121;
}

.coverage-header {
    color: black;
}

.routes svg text,
.routes svg a {
    fill: white;
}
.routes svg rect {
    fill: #212121 !important;
}

.navbar-default,
.btn-default {
    background: #fafafa;
    border-color: #444;
    color: #212121;
}

.navbar-default .navbar-brand {
    color: #212121;
}

.overview .card,
.modules .card {
    background: #fafafa;
    color: #212121;
    border: 1px solid #444;
}
.overview .card a {
    color: #212121;
}

.modules .card-header {
    background: none;
    border-bottom: 1px solid #444;
}

.module .list-group-item {
    background: none;
    border: 1px solid #444;
}

.container-fluid.module h3 a {
    color: #337ab7;
}

table.params thead {
    background: #fafafa;
    color: #212121;
}